Create a report from a ClusterSet and Seurat objects

Create a report from a ClusterSet experiment and Seurat object. If is_spatial_exp argument is set to TRUE Spatial diagram will be added. The function can call Gemini IA to try to guess cell type and functions associated to each gene module. NB: When dealing with large dataset (large number of cells/spots), it is advisable not activate interactive heatmap by deleting "module_iheatmap" from the 'section' argument.

gm_report(
  cluster_set = NULL,
  seurat_object = NULL,
  seurat_assay = NULL,
  seurat_layer = NULL,
  is_spatial_exp = FALSE,
  annotation_src = c("BP", "CC", "MF"),
  report_title = "Gene module report",
  report_subtitle = "An example experiment",
  report_author = "Undefined",
  report_date = format(Sys.time(), "%d %B %Y"),
  out_dir = file.path(fs::path_home(), "gm_book"),
  experimenters = data.frame(),
  workflow_params = data.frame(),
  bioc_org_db = NULL,
  api_key = NULL,
  smp_species = NULL,
  smp_stage = NULL,
  smp_organ = NULL,
  smp_region = NULL,
  sample_gg_heatmap = TRUE,
  rmd_dir = file.path(system.file(package = "scigenex"), "rmarkdown"),
  add_module_score_params = list(nbin = 16, ctrl = 100, name = "MOD_", slot = "data"),
  plot_profiles_params = list(to_lin = TRUE, averaged = TRUE),
  plot_multi_profiles_params = list(legend_name = "Gene\nModule", center = FALSE),
  FeaturePlot_params = list(cols = RColorBrewer::brewer.pal(3, "BuPu"), label = TRUE,
    label.size = 4, repel = TRUE, reduction = "umap", split.by = "orig.ident"),
  SpatialFeaturePlot_params = list(pt.size.factor = 1.7),
  SpatialDimPlot_params = list(pt.size.factor = 1.7),
  DimPlot_params = list(label = TRUE, label.size = 4, repel = TRUE, split.by =
    "orig.ident", reduction = "umap"),
  plot_ggheatmap_params = list(use_top_genes = FALSE, hide_gene_name = TRUE, xlab =
    "Cells/Spots", ylab = "Genes"),
  subsample_by_ident_params = list(nbcell = 200),
  plot_heatmap_params = list(link = "complete", use_top_genes = FALSE, interactive =
    TRUE, line_size_horizontal = 1, label_size = 7),
  cnetplot_params = list(color.params = list(edge = TRUE), showCategory = 6, cex.params =
    list(category_label = 0.6, gene_label = 0.7)),
  vlnPlot_params = list(split.by = "orig.ident", pt.size = 0),
  DotPlot_params = list(split.by = "orig.ident", cols = c("yellow3", "red")),
  color_split =
    RColorBrewer::brewer.pal(length(unique(seurat_object@meta.data$orig.ident)), name =
    "Set1"),
  rm_tmpdir = TRUE,
  section = c("exp_info", "exp_metadata", "exp_experimenters", "exp_sample",
    "exp_params", "exp_stats", "exp_genes", "exp_heatmap", "exp_pca", "exp_elbow",
    "exp_umap", "exp_metrics", "exp_pop", "exp_pop_table", "exp_pop_by_ori",
    "exp_pop_table_by_ori", "exp_spatial_dist", "exp_spatial_dimplot", "exp_mean_1",
    "exp_mean_2", "module_spatial", "module_heatmap", "module_iheatmap", "module_umap",
    "module_umap_by_ori", "module_violin", "module_violin_by_ori", "module_dotplot",
    "module_dotplot_by_ori", "module_genes", 
     "module_cell_annot_IA",
    "module_term_network", "module_term_barplot_1", "module_term_barplot_2",
    "module_term_network_circ", "term_table"),
  quiet = FALSE
)

Arguments

cluster_set

A clusterSet object.

seurat_object

Seurat object.

seurat_assay

Which assay should be used in the Seurat object.

seurat_layer

Which layer should be used in the Seurat object.

is_spatial_exp

Whether there are some spatial information in the ClusterSet object.

annotation_src

The sources of functional annotation (currently a vector taken from "BP", "CC", "MF").

report_title

A title for the report.

report_subtitle

A subtitle for the report.

report_author

A character string corresponding to one or several authors.

report_date

A date.

out_dir

A directory where to store the bookdown output.

experimenters

A data.frame providing information about experimenters.

workflow_params

A data.frame indicating some workflow parameters.

bioc_org_db

A gene annotation database as provided by Bioconductor (e.g. org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, o rg.Dm.eg.db, org.Dr.eg.db, org.Sc.sgd.db, org.Ce.eg.db...). If NULL, module analysis related to functional annotation are canceled.

api_key

An API key for Gemini to perform cell type / cell function analysis. If NULL, the 'module_cell_annot_IA' section will be skipped.

smp_species

The species of the sample (free text). E.g 'Homo sapiens'.

smp_stage

Development stage of the sample (free text). E.g. 'adult'.

smp_organ

The sample organ (free text). E.g. 'tonsil'.

smp_region

A region in the organ. E.g. 'whole' (which will merge as 'whole tonsil').

sample_gg_heatmap

If true, apply cell/spot sample using subsample_by_ident() not only to interactive heatmap but also heatmaps produced by plot_ggheatmap(). It helps reduce the memory footprints.

rmd_dir

A path where to find the templates for creating the book.

add_module_score_params

Some parameters for Seurat::add_module_score() function.

plot_profiles_params

Some parameters for plot_profiles() function

plot_multi_profiles_params

Some parameters for plot_profiles_multi() function.

FeaturePlot_params

Some parameters for Seurat::FeaturePlot() function.

SpatialFeaturePlot_params

Some parameters for Seurat::SpatialFeaturePlot() function.

SpatialDimPlot_params

Some parameters for Seurat::SpatialDimPlot() function.

DimPlot_params

Some parameters for Seurat::DimPlot() function.

plot_ggheatmap_params

Some parameters for plot_ggheatmap() function.

subsample_by_ident_params

The number of cell to take per cell type when subsampling the data for plotting interactive heatmap. Reduce this number if you have a large dataset (e.g. > 10000 cells/spots). Otherwise the dataset will be too large to be handled by the web browser.

plot_heatmap_params

Some parameters for plot_heatmap() function.

cnetplot_params

Some parameters for enrichplot:::cnetplot.enrichResult() function.

vlnPlot_params

The parameters for Seurat::VlnPlot().

rm_tmpdir

Whether to delete temporary directory.

section

Which section to activate/deactivate.

quiet

Whether to run bookdown::render_book() quietly.

Value

No return value. A report is generated and written to the specified output directory.

Examples

library(scigenex)
library(Seurat)
set_verbosity(3)
load_example_dataset('7871581/files/pbmc3k_medium_clusters')
#> |-- INFO :  Dataset 7871581/files/pbmc3k_medium_clusters was already loaded. 
load_example_dataset('7871581/files/pbmc3k_medium')
#> |-- INFO :  Dataset 7871581/files/pbmc3k_medium was already loaded. 
gm_report(pbmc3k_medium_clusters[1:2,], 
                pbmc3k_medium, 
                smp_species="Homo_sapiens", 
                annotation_src="CC",
                smp_region="total", 
                smp_organ="blood", 
                smp_stage="adult", 
                bioc_org_db="org.Hs.eg.db",
                api_key=NULL)
#> |-- DEBUG :  Checking seurat object. 
#> |-- DEBUG :  Checking ClusterSet format. 
#> 
#> Attaching package: ‘BiocGenerics’
#> The following object is masked from ‘package:SeuratObject’:
#> 
#>     intersect
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
#>     union, unique, unsplit, which.max, which.min
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> 
#> Attaching package: ‘IRanges’
#> The following object is masked from ‘package:sp’:
#> 
#>     %over%
#> |-- INFO :  This is not a ST experiment... 
#> |-- INFO :  Canceling ST reporting module. 
#> |-- INFO :  No Gemini key provided... 
#> |-- INFO :  Canceling IA-based cell type annotation. 
#> |-- INFO :  Computing module scores... 
#> |-- DEBUG :  Calling AddModuleScore()... 
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- DEBUG :  Created temporary directory: 
#> |-- INFO :  /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-57-27-2025 
#> |-- DEBUG :  Copying file in temporary directory. 
#> |-- INFO :  The temporary dir contains file: _bookdown.yml 
#> |-- INFO :  The temporary dir contains file: _main.Rmd 
#> |-- INFO :  The temporary dir contains file: footer.Rmd 
#> |-- INFO :  The temporary dir contains file: index.Rmd 
#> |-- INFO :  The temporary dir contains file: module.Rmd 
#> |-- INFO :  The temporary dir contains file: style.css 
#> |-- DEBUG :  Computing top genes. 
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- DEBUG :  Using fast computation of pearson correlations. 
#> |-- INFO :  Extracting genes with the highest mean correlation to the others... 
#> |-- DEBUG :  Using fast computation of pearson correlations. 
#> |-- INFO :  Extracting genes with the highest mean correlation to the others... 
#> |-- INFO :  Results are stored in 'top_genes' slot of the object. 
#> |-- DEBUG :  Computing centers. 
#> |-- INFO :  Computing centers. 
#> |-- DEBUG :  Preparing matrix. 
#> |-- DEBUG :  Renaming columns / rows. 
#> |-- DEBUG :  Looping over clusters... 
#> |-- DEBUG :  Computing cluster 1 center. 
#> |-- DEBUG :  Computing cluster 2 center. 
#> |-- INFO :  Computing semantic similarity (CC) for cnet_plot. 
#> |-- INFO :  Preparing parameters for the report. 
#> |-- INFO :  Looping through parameterised Reports. 
#> |-- DEBUG :  Preparing Rmd files for modules 1 
#> |-- DEBUG :  file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-57-27-2025/rmarkdown/module_0001.Rmd 
#> |-- DEBUG :  Preparation of Rmd files for objects 1 finished. 
#> |-- DEBUG :  Preparing Rmd files for modules 2 
#> |-- DEBUG :  file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-57-27-2025/rmarkdown/module_0002.Rmd 
#> |-- DEBUG :  Preparation of Rmd files for objects 2 finished. 
#> |-- INFO :  Deleting sample.Rmd. 
#> |-- INFO :  preparing _bookdown.yml 
#> Rendering book in directory '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-57-27-2025/rmarkdown'
#> 
#> 
#> processing file: _main.Rmd
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#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 1/319                            
#> 2/319 [start]                    
#> 3/319                            
#> 4/319 [unnamed-chunk-1]          
#> 5/319                            
#> 6/319 [unnamed-chunk-2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 7/319                            
#> 8/319 [section_gen_info_1]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 9/319                            
#> 10/319 [section_gen_info_2]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 11/319                            
#> 12/319 [section_gen_info_3]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 13/319                            
#> 14/319 [section_gen_info_4]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 15/319                            
#> 16/319 [parameters]               
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 17/319                            
#> 18/319 [section_gen_info_5]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 19/319                            
#> 20/319 [section_gen_info_6]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 21/319                            
#> 22/319 [section_gen_info_7]       
#> 23/319                            
#> 24/319 [section_gen_info_8]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 25/319                            
#> 26/319 [section_gen_info_9]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 27/319                            
#> 28/319 [section_gen_info_10]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 29/319                            
#> 30/319 [section_gen_info_11]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 31/319                            
#> 32/319 [section_gen_info_12]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 33/319                            
#> 34/319 [section_gen_info_13]      
#> 35/319                            
#> 36/319 [section_gen_info_14]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 37/319                            
#> 38/319 [section_gen_info_14a]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 39/319                            
#> 40/319 [section_gen_info_14b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 41/319                            
#> 42/319 [section_gen_info_14c]     
#> 43/319                            
#> 44/319 [section_gen_info_14d]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 45/319                            
#> 46/319 [section_gen_info_14e]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 47/319                            
#> 48/319 [section_gen_info_14f]     
#> 49/319                            
#> 50/319 [section_gen_info_15]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 51/319                            
#> 52/319 [section_gen_info_16]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 53/319                            
#> 54/319 [section_gen_info_17]      
#> 55/319                            
#> 56/319 [section_gen_info_15_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 57/319                            
#> 58/319 [section_gen_info_16_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 59/319                            
#> 60/319 [section_gen_info_17_1]    
#> 61/319                            
#> 62/319 [section_gen_info_17a]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 63/319                            
#> 64/319 [section_gen_info_17b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 65/319                            
#> 66/319 [section_gen_info_17c]     
#> 67/319                            
#> 68/319 [section_gen_info_17d]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 69/319                            
#> 70/319 [section_gen_info_17e]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 71/319                            
#> 72/319 [section_gen_info_17f]     
#> 73/319                            
#> 74/319 [section_gen_info_17d-3]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 75/319                            
#> 76/319 [section_gen_info_17e-4]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 77/319                            
#> 78/319 [section_gen_info_17f-5]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 79/319                            
#> 80/319 [section_gen_info_17d_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 81/319                            
#> 82/319 [section_gen_info_17e_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 83/319                            
#> 84/319 [section_gen_info_17f_1]   
#> 85/319                            
#> 86/319 [section_gen_info_17d_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 87/319                            
#> 88/319 [section_gen_info_17e_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 89/319                            
#> 90/319 [section_gen_info_17f_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 91/319                            
#> 92/319 [section_gen_info_18]      
#> 93/319                            
#> 94/319 [section_gen_info_19]      
#> 95/319                            
#> 96/319 [section_gen_info_20]      
#> 97/319                            
#> 98/319 [section_gen_info_21]      
#> 99/319                            
#> 100/319 [section_gen_info_22]      
#> 101/319                            
#> 102/319 [section_gen_info_23]      
#> 103/319                            
#> 104/319 [section_gen_info_24]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 105/319                            
#> 106/319 [section_gen_info_25]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 107/319                            
#> 108/319 [section_gen_info_26]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 109/319                            
#> 110/319 [section_gen_info_27]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 111/319                            
#> 112/319 [section_gen_info_28]      
#> 113/319                            
#> 114/319 [section_gen_info_29]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 115/319                            
#> 116/319 [section_gen_info_30]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 117/319                            
#> 118/319 [section_gen_info_31]      
#> 119/319                            
#> 120/319 [section_gen_info_32_table]
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 121/319                            
#> 122/319 [section_gen_info_33]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 123/319                            
#> 124/319 [section_gen_info_34]      
#> 125/319                            
#> 126/319 [section_gen_info_34b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 127/319                            
#> 128/319 [section_gen_info_35]      
#> 129/319                            
#> 130/319 [section_gen_info_35b]     
#> 131/319                            
#> 132/319 [section_gen_info_36]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 133/319                            
#> 134/319 [section_gen_info_37]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 135/319                            
#> 136/319 [section_gen_info_38]      
#> 137/319                            
#> 138/319 [section_gen_info_39]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 139/319                            
#> 140/319 [section_gen_info_40]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 141/319                            
#> 142/319 [section_gen_info_41]      
#> 143/319                            
#> 144/319 [unnamed-chunk-6]          
#> 145/319                            
#> 146/319 [unnamed-chunk-7]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 147/319                            
#> 148/319 [start_MOD_1]              
#> 149/319                            
#> 150/319 [level_0_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 151/319                            
#> 152/319 [level_0b_MOD_1]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 153/319                            
#> 154/319 [level_1_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 155/319                            
#> 156/319 [heatmap_2_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 157/319                            
#> 158/319 [spatial_0_MOD_1]          
#> 159/319                            
#> 160/319 [spatial_1_MOD_1]          
#> 161/319                            
#> 162/319 [spatial_2_MOD_1]          
#> 163/319                            
#> 164/319 [heatmap_3_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 165/319                            
#> 166/319 [heatmap_4_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 167/319                            
#> 168/319 [heatmap_5_MOD_1]          
#> 169/319                            
#> 170/319 [iheatmap_2_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 171/319                            
#> 172/319 [iheatmap_3_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 173/319                            
#> 174/319 [iheatmap_4_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 175/319                            
#> 176/319 [iumap_2_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 177/319                            
#> 178/319 [iumap_3_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 179/319                            
#> 180/319 [iumap_4_MOD_1]            
#> 181/319                            
#> 182/319 [iumap_2_1_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 183/319                            
#> 184/319 [iumap_3_1_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 185/319                            
#> 186/319 [iumap_4_1_MOD_1]          
#> 187/319                            
#> 188/319 [violin_2_MOD_1]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 189/319                            
#> 190/319 [violin_3_MOD_1]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 191/319                            
#> 192/319 [violin_4_MOD_1]           
#> 193/319                            
#> 194/319 [violin_by_ori_2_MOD_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 195/319                            
#> 196/319 [violin_by_ori_3_MOD_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 197/319                            
#> 198/319 [violin_by_ori_4_MOD_1]    
#> 199/319                            
#> 200/319 [dotplot_2_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 201/319                            
#> 202/319 [dotplot_3_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 203/319                            
#> 204/319 [dotplot_4_MOD_1]          
#> 205/319                            
#> 206/319 [dotplot_by_ori_2_MOD_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 207/319                            
#> 208/319 [dotplot_by_ori_3_MOD_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 209/319                            
#> 210/319 [dotplot_by_ori_4_MOD_1]   
#> 211/319                            
#> 212/319 [gene_info_1_MOD_1]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 213/319                            
#> 214/319 [gene_info_2_MOD_1]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 215/319                            
#> 216/319 [gene_info_3_MOD_1]        
#> 217/319                            
#> 218/319 [gene_info_4_MOD_1]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 219/319                            
#> 220/319 [level_2_MOD_1]            
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#> 229/319                            
#> 230/319 [unnamed-chunk-8]          
#> 231/319                            
#> 232/319 [unnamed-chunk-9]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 233/319                            
#> 234/319 [start_MOD_2]              
#> 235/319                            
#> 236/319 [level_0_MOD_2]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 237/319                            
#> 238/319 [level_0b_MOD_2]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 239/319                            
#> 240/319 [level_1_MOD_2]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 241/319                            
#> 242/319 [heatmap_2_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 243/319                            
#> 244/319 [spatial_0_MOD_2]          
#> 245/319                            
#> 246/319 [spatial_1_MOD_2]          
#> 247/319                            
#> 248/319 [spatial_2_MOD_2]          
#> 249/319                            
#> 250/319 [heatmap_3_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 251/319                            
#> 252/319 [heatmap_4_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 253/319                            
#> 254/319 [heatmap_5_MOD_2]          
#> 255/319                            
#> 256/319 [iheatmap_2_MOD_2]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 257/319                            
#> 258/319 [iheatmap_3_MOD_2]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 259/319                            
#> 260/319 [iheatmap_4_MOD_2]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 261/319                            
#> 262/319 [iumap_2_MOD_2]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 263/319                            
#> 264/319 [iumap_3_MOD_2]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 265/319                            
#> 266/319 [iumap_4_MOD_2]            
#> 267/319                            
#> 268/319 [iumap_2_1_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 269/319                            
#> 270/319 [iumap_3_1_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 271/319                            
#> 272/319 [iumap_4_1_MOD_2]          
#> 273/319                            
#> 274/319 [violin_2_MOD_2]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 275/319                            
#> 276/319 [violin_3_MOD_2]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 277/319                            
#> 278/319 [violin_4_MOD_2]           
#> 279/319                            
#> 280/319 [violin_by_ori_2_MOD_2]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 281/319                            
#> 282/319 [violin_by_ori_3_MOD_2]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 283/319                            
#> 284/319 [violin_by_ori_4_MOD_2]    
#> 285/319                            
#> 286/319 [dotplot_2_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 287/319                            
#> 288/319 [dotplot_3_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 289/319                            
#> 290/319 [dotplot_4_MOD_2]          
#> 291/319                            
#> 292/319 [dotplot_by_ori_2_MOD_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 293/319                            
#> 294/319 [dotplot_by_ori_3_MOD_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 295/319                            
#> 296/319 [dotplot_by_ori_4_MOD_2]   
#> 297/319                            
#> 298/319 [gene_info_1_MOD_2]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 299/319                            
#> 300/319 [gene_info_2_MOD_2]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 301/319                            
#> 302/319 [gene_info_3_MOD_2]        
#> 303/319                            
#> 304/319 [gene_info_4_MOD_2]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 305/319                            
#> 306/319 [level_2_MOD_2]            
#> 307/319                            
#> 308/319 [cell_annot_IA_1_MOD_2]    
#> 309/319                            
#> 310/319 [cell_annot_IA_2_MOD_2]    
#> 311/319                            
#> 312/319 [cell_annot_IA_3_MOD_2]    
#> 313/319                            
#> 314/319 [func_anno_MOD_2]          
#> 315/319                            
#> 316/319 [session_info]             
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 317/319                            
#> 318/319 [panel_setup_final]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 319/319                            
#> output file: _main.knit.md
#> /usr/local/bin/pandoc +RTS -K512m -RTS _main.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _main.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/table-classes.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6O/file6c207857009b --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 2 --template /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --css style.css --mathjax --include-in-header /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6O/rmarkdown-str6c206f94ddca.html 
#> 
#> Output created: _book/index.html
#> |-- INFO :  Results have been copied to: /Users/puthier/gm_book 
set_verbosity(3)
load_example_dataset('7870305/files/lymph_node_tiny_clusters_2')
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_clusters_2 was already loaded. 
load_example_dataset('7870305/files/lymph_node_tiny_2')
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_2 was already loaded. 
gm_report(lymph_node_tiny_clusters_2[1:2,], 
                lymph_node_tiny_2, 
                smp_species="Homo sapiens", 
                smp_region="total", 
                smp_organ="lymph node", 
                smp_stage="adult", 
                annotation_src="CC",
                bioc_org_db="org.Hs.eg.db",
                api_key=NULL,
                is_spatial_exp=TRUE,
                SpatialFeaturePlot_params=list(pt.size.factor = 3000), # adapt the point size as
                SpatialDimPlot_params=list(pt.size.factor = 3000))     # the object was created with an older seurat version
#> |-- DEBUG :  Checking seurat object. 
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- INFO :  No Gemini key provided... 
#> |-- INFO :  Canceling IA-based cell type annotation. 
#> |-- INFO :  Computing module scores... 
#> |-- DEBUG :  Calling AddModuleScore()... 
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- DEBUG :  Created temporary directory: 
#> |-- INFO :  /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-58-38-2025 
#> |-- DEBUG :  Copying file in temporary directory. 
#> |-- INFO :  The temporary dir contains file: _bookdown.yml 
#> |-- INFO :  The temporary dir contains file: _main.Rmd 
#> |-- INFO :  The temporary dir contains file: footer.Rmd 
#> |-- INFO :  The temporary dir contains file: index.Rmd 
#> |-- INFO :  The temporary dir contains file: module.Rmd 
#> |-- INFO :  The temporary dir contains file: style.css 
#> |-- DEBUG :  Computing top genes. 
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- DEBUG :  Using fast computation of pearson correlations. 
#> |-- INFO :  Extracting genes with the highest mean correlation to the others... 
#> |-- DEBUG :  Using fast computation of pearson correlations. 
#> |-- INFO :  Extracting genes with the highest mean correlation to the others... 
#> |-- INFO :  Results are stored in 'top_genes' slot of the object. 
#> |-- DEBUG :  Computing centers. 
#> |-- INFO :  Computing centers. 
#> |-- DEBUG :  Preparing matrix. 
#> |-- DEBUG :  Renaming columns / rows. 
#> |-- DEBUG :  Looping over clusters... 
#> |-- DEBUG :  Computing cluster 1 center. 
#> |-- DEBUG :  Computing cluster 2 center. 
#> |-- INFO :  Computing semantic similarity (CC) for cnet_plot. 
#> |-- INFO :  Preparing parameters for the report. 
#> |-- INFO :  Looping through parameterised Reports. 
#> |-- DEBUG :  Preparing Rmd files for modules 1 
#> |-- DEBUG :  file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-58-38-2025/rmarkdown/module_0001.Rmd 
#> |-- DEBUG :  Preparation of Rmd files for objects 1 finished. 
#> |-- DEBUG :  Preparing Rmd files for modules 2 
#> |-- DEBUG :  file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-58-38-2025/rmarkdown/module_0002.Rmd 
#> |-- DEBUG :  Preparation of Rmd files for objects 2 finished. 
#> |-- INFO :  Deleting sample.Rmd. 
#> |-- INFO :  preparing _bookdown.yml 
#> Rendering book in directory '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-58-38-2025/rmarkdown'
#> 
#> 
#> processing file: _main.Rmd
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 1/319                            
#> 2/319 [start]                    
#> 3/319                            
#> 4/319 [unnamed-chunk-1]          
#> 5/319                            
#> 6/319 [unnamed-chunk-2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 7/319                            
#> 8/319 [section_gen_info_1]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 9/319                            
#> 10/319 [section_gen_info_2]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 11/319                            
#> 12/319 [section_gen_info_3]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 13/319                            
#> 14/319 [section_gen_info_4]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 15/319                            
#> 16/319 [parameters]               
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 17/319                            
#> 18/319 [section_gen_info_5]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 19/319                            
#> 20/319 [section_gen_info_6]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 21/319                            
#> 22/319 [section_gen_info_7]       
#> 23/319                            
#> 24/319 [section_gen_info_8]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 25/319                            
#> 26/319 [section_gen_info_9]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 27/319                            
#> 28/319 [section_gen_info_10]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 29/319                            
#> 30/319 [section_gen_info_11]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 31/319                            
#> 32/319 [section_gen_info_12]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 33/319                            
#> 34/319 [section_gen_info_13]      
#> 35/319                            
#> 36/319 [section_gen_info_14]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 37/319                            
#> 38/319 [section_gen_info_14a]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 39/319                            
#> 40/319 [section_gen_info_14b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 41/319                            
#> 42/319 [section_gen_info_14c]     
#> 43/319                            
#> 44/319 [section_gen_info_14d]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 45/319                            
#> 46/319 [section_gen_info_14e]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 47/319                            
#> 48/319 [section_gen_info_14f]     
#> 49/319                            
#> 50/319 [section_gen_info_15]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 51/319                            
#> 52/319 [section_gen_info_16]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 53/319                            
#> 54/319 [section_gen_info_17]      
#> 55/319                            
#> 56/319 [section_gen_info_15_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 57/319                            
#> 58/319 [section_gen_info_16_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 59/319                            
#> 60/319 [section_gen_info_17_1]    
#> 61/319                            
#> 62/319 [section_gen_info_17a]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 63/319                            
#> 64/319 [section_gen_info_17b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 65/319                            
#> 66/319 [section_gen_info_17c]     
#> 67/319                            
#> 68/319 [section_gen_info_17d]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 69/319                            
#> 70/319 [section_gen_info_17e]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 71/319                            
#> 72/319 [section_gen_info_17f]     
#> 73/319                            
#> 74/319 [section_gen_info_17d-3]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 75/319                            
#> 76/319 [section_gen_info_17e-4]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 77/319                            
#> 78/319 [section_gen_info_17f-5]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 79/319                            
#> 80/319 [section_gen_info_17d_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 81/319                            
#> 82/319 [section_gen_info_17e_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 83/319                            
#> 84/319 [section_gen_info_17f_1]   
#> 85/319                            
#> 86/319 [section_gen_info_17d_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 87/319                            
#> 88/319 [section_gen_info_17e_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 89/319                            
#> 90/319 [section_gen_info_17f_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 91/319                            
#> 92/319 [section_gen_info_18]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 93/319                            
#> 94/319 [section_gen_info_19]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 95/319                            
#> 96/319 [section_gen_info_20]      
#> 97/319                            
#> 98/319 [section_gen_info_21]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 99/319                            
#> 100/319 [section_gen_info_22]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 101/319                            
#> 102/319 [section_gen_info_23]      
#> 103/319                            
#> 104/319 [section_gen_info_24]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 105/319                            
#> 106/319 [section_gen_info_25]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 107/319                            
#> 108/319 [section_gen_info_26]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 109/319                            
#> 110/319 [section_gen_info_27]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 111/319                            
#> 112/319 [section_gen_info_28]      
#> 113/319                            
#> 114/319 [section_gen_info_29]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 115/319                            
#> 116/319 [section_gen_info_30]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 117/319                            
#> 118/319 [section_gen_info_31]      
#> 119/319                            
#> 120/319 [section_gen_info_32_table]
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 121/319                            
#> 122/319 [section_gen_info_33]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 123/319                            
#> 124/319 [section_gen_info_34]      
#> 125/319                            
#> 126/319 [section_gen_info_34b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 127/319                            
#> 128/319 [section_gen_info_35]      
#> 129/319                            
#> 130/319 [section_gen_info_35b]     
#> 131/319                            
#> 132/319 [section_gen_info_36]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 133/319                            
#> 134/319 [section_gen_info_37]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 135/319                            
#> 136/319 [section_gen_info_38]      
#> 137/319                            
#> 138/319 [section_gen_info_39]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 139/319                            
#> 140/319 [section_gen_info_40]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 141/319                            
#> 142/319 [section_gen_info_41]      
#> 143/319                            
#> 144/319 [unnamed-chunk-6]          
#> 145/319                            
#> 146/319 [unnamed-chunk-7]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 147/319                            
#> 148/319 [start_MOD_1]              
#> 149/319                            
#> 150/319 [level_0_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 151/319                            
#> 152/319 [level_0b_MOD_1]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 153/319                            
#> 154/319 [level_1_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 155/319                            
#> 156/319 [heatmap_2_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 157/319                            
#> 158/319 [spatial_0_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 159/319                            
#> 160/319 [spatial_1_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 161/319                            
#> 162/319 [spatial_2_MOD_1]          
#> 163/319                            
#> 164/319 [heatmap_3_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 165/319                            
#> 166/319 [heatmap_4_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 167/319                            
#> 168/319 [heatmap_5_MOD_1]          
#> 169/319                            
#> 170/319 [iheatmap_2_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 171/319                            
#> 172/319 [iheatmap_3_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 173/319                            
#> 174/319 [iheatmap_4_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 175/319                            
#> 176/319 [iumap_2_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 177/319                            
#> 178/319 [iumap_3_MOD_1]            
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#> Warning: 'xfun::attr()' is deprecated.
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#> 233/319                            
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#> Warning: 'xfun::attr()' is deprecated.
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#> See help("Deprecated")
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#> 241/319                            
#> 242/319 [heatmap_2_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
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#> See help("Deprecated")
#> 243/319                            
#> 244/319 [spatial_0_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
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#> See help("Deprecated")
#> 245/319                            
#> 246/319 [spatial_1_MOD_2]          
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#> See help("Deprecated")
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#> 252/319 [heatmap_4_MOD_2]          
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#> See help("Deprecated")
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#> 255/319                            
#> 256/319 [iheatmap_2_MOD_2]         
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#> 257/319                            
#> 258/319 [iheatmap_3_MOD_2]         
#> Warning: 'xfun::attr()' is deprecated.
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#> See help("Deprecated")
#> 259/319                            
#> 260/319 [iheatmap_4_MOD_2]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
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#> 261/319                            
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#> See help("Deprecated")
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#> 273/319                            
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#> See help("Deprecated")
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#> 287/319                            
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#> See help("Deprecated")
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#> See help("Deprecated")
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#> 294/319 [dotplot_by_ori_3_MOD_2]   
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#> 303/319                            
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#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
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#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 305/319                            
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#> 315/319                            
#> 316/319 [session_info]             
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 317/319                            
#> 318/319 [panel_setup_final]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 319/319                            
#> output file: _main.knit.md
#> /usr/local/bin/pandoc +RTS -K512m -RTS _main.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _main.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/table-classes.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6O/file6c20166d3201 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 2 --template /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --css style.css --mathjax --include-in-header /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6O/rmarkdown-str6c2060533f7f.html 
#> 
#> Output created: _book/index.html
#> |-- INFO :  Results have been copied to: /Users/puthier/gm_book 
set_verbosity(3)
markers <- Seurat::FindAllMarkers(lymph_node_tiny_2, only.pos = TRUE)
#> Calculating cluster 0
#> Calculating cluster 1
#> Calculating cluster 2
#> Calculating cluster 3
#> Calculating cluster 4
#> Calculating cluster 5
#> Calculating cluster 6
#> Calculating cluster 7
#> Calculating cluster 8
#> Calculating cluster 9
#> Calculating cluster 10
#> Calculating cluster 11
#> Calculating cluster 12
cs <- cluster_set_from_seurat(lymph_node_tiny_2, markers, p_val_adj=0.001, assay="Spatial")
#> |-- DEBUG :  Converting a Seurat object from cluster_set... 
#> |-- INFO :  This seurat object contains the following assay : Spatial. 
#> |-- DEBUG :  Selecting  markers based on p_val_adj... 
#> |-- DEBUG :  Disambiguating gene duplicates using '~' separator 
#> |-- DEBUG :  There are duplicated gene names, handling them... 
#> |-- DEBUG :  The maximum number of duplicates for one gene is : 2. 
#> |-- DEBUG :  Looping though duplicate : 1. 
#> |-- DEBUG :  Adding 17 genes to the matrix. 
#> |-- DEBUG :  Subsetting... 
#> |-- DEBUG :  Binding... 
#> |-- DEBUG :  Looping though duplicate : 2. 
#> |-- DEBUG :  Adding 2 genes to the matrix. 
#> |-- DEBUG :  Subsetting... 
#> |-- DEBUG :  Binding... 
#> |-- INFO :  Computing centers. 
#> |-- DEBUG :  Preparing matrix. 
#> |-- DEBUG :  Renaming columns / rows. 
#> |-- DEBUG :  Looping over clusters... 
#> |-- DEBUG :  Computing cluster 1 center. 
#> |-- DEBUG :  Computing cluster 2 center. 
#> |-- DEBUG :  Computing cluster 3 center. 
#> |-- DEBUG :  Computing cluster 4 center. 
#> |-- DEBUG :  Computing cluster 5 center. 
#> |-- DEBUG :  Computing cluster 6 center. 
#> |-- DEBUG :  Computing cluster 7 center. 
#> |-- DEBUG :  Computing cluster 8 center. 
#> |-- DEBUG :  Computing cluster 9 center. 
#> |-- DEBUG :  Computing cluster 10 center. 
#> |-- DEBUG :  Computing cluster 11 center. 
gm_report(cs[1:2,], 
                lymph_node_tiny_2, 
                smp_species="Homo sapiens", 
                smp_region="total", 
                smp_organ="lymph node", 
                smp_stage="adult", 
                annotation_src="CC",
                is_spatial_exp=TRUE,
                sample_gg_heatmap=TRUE,
                subsample_by_ident_params=list(nbcell=20),
                bioc_org_db="org.Hs.eg.db",
                SpatialFeaturePlot_params=list(pt.size.factor = 3000), # adapt the point size as
                SpatialDimPlot_params=list(pt.size.factor = 3000),     # the object was created with an older seurat version
                api_key=NULL) 
#> |-- DEBUG :  Checking seurat object. 
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- INFO :  No Gemini key provided... 
#> |-- INFO :  Canceling IA-based cell type annotation. 
#> |-- INFO :  Computing module scores... 
#> |-- DEBUG :  Calling AddModuleScore()... 
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- DEBUG :  Created temporary directory: 
#> |-- INFO :  /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-59-53-2025 
#> |-- DEBUG :  Copying file in temporary directory. 
#> |-- INFO :  The temporary dir contains file: _bookdown.yml 
#> |-- INFO :  The temporary dir contains file: _main.Rmd 
#> |-- INFO :  The temporary dir contains file: footer.Rmd 
#> |-- INFO :  The temporary dir contains file: index.Rmd 
#> |-- INFO :  The temporary dir contains file: module.Rmd 
#> |-- INFO :  The temporary dir contains file: style.css 
#> |-- DEBUG :  Computing top genes. 
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- INFO :  One or several clusters contain less than 20 genes. Retrieving all genes 
#> |-- DEBUG :  Using fast computation of pearson correlations. 
#> |-- INFO :  Extracting genes with the highest mean correlation to the others... 
#> |-- INFO :  Results are stored in 'top_genes' slot of the object. 
#> |-- DEBUG :  Computing centers. 
#> |-- INFO :  Computing centers. 
#> |-- DEBUG :  Preparing matrix. 
#> |-- DEBUG :  Renaming columns / rows. 
#> |-- DEBUG :  Looping over clusters... 
#> |-- DEBUG :  Computing cluster 1 center. 
#> |-- DEBUG :  Computing cluster 2 center. 
#> |-- INFO :  Computing semantic similarity (CC) for cnet_plot. 
#> |-- INFO :  Preparing parameters for the report. 
#> |-- INFO :  Looping through parameterised Reports. 
#> |-- DEBUG :  Preparing Rmd files for modules 1 
#> |-- DEBUG :  file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-59-53-2025/rmarkdown/module_0001.Rmd 
#> |-- DEBUG :  Preparation of Rmd files for objects 1 finished. 
#> |-- DEBUG :  Preparing Rmd files for modules 2 
#> |-- DEBUG :  file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-59-53-2025/rmarkdown/module_0002.Rmd 
#> |-- DEBUG :  Preparation of Rmd files for objects 2 finished. 
#> |-- INFO :  Deleting sample.Rmd. 
#> |-- INFO :  preparing _bookdown.yml 
#> Rendering book in directory '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6OWed-Oct-11-59-53-2025/rmarkdown'
#> 
#> 
#> processing file: _main.Rmd
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 1/319                            
#> 2/319 [start]                    
#> 3/319                            
#> 4/319 [unnamed-chunk-1]          
#> 5/319                            
#> 6/319 [unnamed-chunk-2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 7/319                            
#> 8/319 [section_gen_info_1]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 9/319                            
#> 10/319 [section_gen_info_2]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 11/319                            
#> 12/319 [section_gen_info_3]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 13/319                            
#> 14/319 [section_gen_info_4]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 15/319                            
#> 16/319 [parameters]               
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 17/319                            
#> 18/319 [section_gen_info_5]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 19/319                            
#> 20/319 [section_gen_info_6]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 21/319                            
#> 22/319 [section_gen_info_7]       
#> 23/319                            
#> 24/319 [section_gen_info_8]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 25/319                            
#> 26/319 [section_gen_info_9]       
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 27/319                            
#> 28/319 [section_gen_info_10]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 29/319                            
#> 30/319 [section_gen_info_11]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 31/319                            
#> 32/319 [section_gen_info_12]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 33/319                            
#> 34/319 [section_gen_info_13]      
#> 35/319                            
#> 36/319 [section_gen_info_14]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 37/319                            
#> 38/319 [section_gen_info_14a]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 39/319                            
#> 40/319 [section_gen_info_14b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 41/319                            
#> 42/319 [section_gen_info_14c]     
#> 43/319                            
#> 44/319 [section_gen_info_14d]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 45/319                            
#> 46/319 [section_gen_info_14e]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 47/319                            
#> 48/319 [section_gen_info_14f]     
#> 49/319                            
#> 50/319 [section_gen_info_15]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 51/319                            
#> 52/319 [section_gen_info_16]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 53/319                            
#> 54/319 [section_gen_info_17]      
#> 55/319                            
#> 56/319 [section_gen_info_15_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 57/319                            
#> 58/319 [section_gen_info_16_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 59/319                            
#> 60/319 [section_gen_info_17_1]    
#> 61/319                            
#> 62/319 [section_gen_info_17a]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 63/319                            
#> 64/319 [section_gen_info_17b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 65/319                            
#> 66/319 [section_gen_info_17c]     
#> 67/319                            
#> 68/319 [section_gen_info_17d]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 69/319                            
#> 70/319 [section_gen_info_17e]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 71/319                            
#> 72/319 [section_gen_info_17f]     
#> 73/319                            
#> 74/319 [section_gen_info_17d-3]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 75/319                            
#> 76/319 [section_gen_info_17e-4]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 77/319                            
#> 78/319 [section_gen_info_17f-5]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 79/319                            
#> 80/319 [section_gen_info_17d_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 81/319                            
#> 82/319 [section_gen_info_17e_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 83/319                            
#> 84/319 [section_gen_info_17f_1]   
#> 85/319                            
#> 86/319 [section_gen_info_17d_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 87/319                            
#> 88/319 [section_gen_info_17e_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 89/319                            
#> 90/319 [section_gen_info_17f_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 91/319                            
#> 92/319 [section_gen_info_18]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 93/319                            
#> 94/319 [section_gen_info_19]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 95/319                            
#> 96/319 [section_gen_info_20]      
#> 97/319                            
#> 98/319 [section_gen_info_21]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 99/319                            
#> 100/319 [section_gen_info_22]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 101/319                            
#> 102/319 [section_gen_info_23]      
#> 103/319                            
#> 104/319 [section_gen_info_24]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 105/319                            
#> 106/319 [section_gen_info_25]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 107/319                            
#> 108/319 [section_gen_info_26]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 109/319                            
#> 110/319 [section_gen_info_27]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 111/319                            
#> 112/319 [section_gen_info_28]      
#> 113/319                            
#> 114/319 [section_gen_info_29]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 115/319                            
#> 116/319 [section_gen_info_30]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 117/319                            
#> 118/319 [section_gen_info_31]      
#> 119/319                            
#> 120/319 [section_gen_info_32_table]
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 121/319                            
#> 122/319 [section_gen_info_33]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 123/319                            
#> 124/319 [section_gen_info_34]      
#> 125/319                            
#> 126/319 [section_gen_info_34b]     
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 127/319                            
#> 128/319 [section_gen_info_35]      
#> 129/319                            
#> 130/319 [section_gen_info_35b]     
#> 131/319                            
#> 132/319 [section_gen_info_36]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 133/319                            
#> 134/319 [section_gen_info_37]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 135/319                            
#> 136/319 [section_gen_info_38]      
#> 137/319                            
#> 138/319 [section_gen_info_39]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 139/319                            
#> 140/319 [section_gen_info_40]      
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 141/319                            
#> 142/319 [section_gen_info_41]      
#> 143/319                            
#> 144/319 [unnamed-chunk-6]          
#> 145/319                            
#> 146/319 [unnamed-chunk-7]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 147/319                            
#> 148/319 [start_MOD_1]              
#> 149/319                            
#> 150/319 [level_0_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 151/319                            
#> 152/319 [level_0b_MOD_1]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 153/319                            
#> 154/319 [level_1_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 155/319                            
#> 156/319 [heatmap_2_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 157/319                            
#> 158/319 [spatial_0_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 159/319                            
#> 160/319 [spatial_1_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 161/319                            
#> 162/319 [spatial_2_MOD_1]          
#> 163/319                            
#> 164/319 [heatmap_3_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 165/319                            
#> 166/319 [heatmap_4_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 167/319                            
#> 168/319 [heatmap_5_MOD_1]          
#> 169/319                            
#> 170/319 [iheatmap_2_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 171/319                            
#> 172/319 [iheatmap_3_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 173/319                            
#> 174/319 [iheatmap_4_MOD_1]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 175/319                            
#> 176/319 [iumap_2_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 177/319                            
#> 178/319 [iumap_3_MOD_1]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 179/319                            
#> 180/319 [iumap_4_MOD_1]            
#> 181/319                            
#> 182/319 [iumap_2_1_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 183/319                            
#> 184/319 [iumap_3_1_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 185/319                            
#> 186/319 [iumap_4_1_MOD_1]          
#> 187/319                            
#> 188/319 [violin_2_MOD_1]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 189/319                            
#> 190/319 [violin_3_MOD_1]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 191/319                            
#> 192/319 [violin_4_MOD_1]           
#> 193/319                            
#> 194/319 [violin_by_ori_2_MOD_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 195/319                            
#> 196/319 [violin_by_ori_3_MOD_1]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 197/319                            
#> 198/319 [violin_by_ori_4_MOD_1]    
#> 199/319                            
#> 200/319 [dotplot_2_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 201/319                            
#> 202/319 [dotplot_3_MOD_1]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 203/319                            
#> 204/319 [dotplot_4_MOD_1]          
#> 205/319                            
#> 206/319 [dotplot_by_ori_2_MOD_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 207/319                            
#> 208/319 [dotplot_by_ori_3_MOD_1]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 209/319                            
#> 210/319 [dotplot_by_ori_4_MOD_1]   
#> 211/319                            
#> 212/319 [gene_info_1_MOD_1]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 213/319                            
#> 214/319 [gene_info_2_MOD_1]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 215/319                            
#> 216/319 [gene_info_3_MOD_1]        
#> 217/319                            
#> 218/319 [gene_info_4_MOD_1]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 219/319                            
#> 220/319 [level_2_MOD_1]            
#> 221/319                            
#> 222/319 [cell_annot_IA_1_MOD_1]    
#> 223/319                            
#> 224/319 [cell_annot_IA_2_MOD_1]    
#> 225/319                            
#> 226/319 [cell_annot_IA_3_MOD_1]    
#> 227/319                            
#> 228/319 [func_anno_MOD_1]          
#> 229/319                            
#> 230/319 [unnamed-chunk-8]          
#> 231/319                            
#> 232/319 [unnamed-chunk-9]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 233/319                            
#> 234/319 [start_MOD_2]              
#> 235/319                            
#> 236/319 [level_0_MOD_2]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 237/319                            
#> 238/319 [level_0b_MOD_2]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 239/319                            
#> 240/319 [level_1_MOD_2]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 241/319                            
#> 242/319 [heatmap_2_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 243/319                            
#> 244/319 [spatial_0_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 245/319                            
#> 246/319 [spatial_1_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 247/319                            
#> 248/319 [spatial_2_MOD_2]          
#> 249/319                            
#> 250/319 [heatmap_3_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 251/319                            
#> 252/319 [heatmap_4_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 253/319                            
#> 254/319 [heatmap_5_MOD_2]          
#> 255/319                            
#> 256/319 [iheatmap_2_MOD_2]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 257/319                            
#> 258/319 [iheatmap_3_MOD_2]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 259/319                            
#> 260/319 [iheatmap_4_MOD_2]         
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 261/319                            
#> 262/319 [iumap_2_MOD_2]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 263/319                            
#> 264/319 [iumap_3_MOD_2]            
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 265/319                            
#> 266/319 [iumap_4_MOD_2]            
#> 267/319                            
#> 268/319 [iumap_2_1_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 269/319                            
#> 270/319 [iumap_3_1_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 271/319                            
#> 272/319 [iumap_4_1_MOD_2]          
#> 273/319                            
#> 274/319 [violin_2_MOD_2]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 275/319                            
#> 276/319 [violin_3_MOD_2]           
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 277/319                            
#> 278/319 [violin_4_MOD_2]           
#> 279/319                            
#> 280/319 [violin_by_ori_2_MOD_2]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 281/319                            
#> 282/319 [violin_by_ori_3_MOD_2]    
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 283/319                            
#> 284/319 [violin_by_ori_4_MOD_2]    
#> 285/319                            
#> 286/319 [dotplot_2_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 287/319                            
#> 288/319 [dotplot_3_MOD_2]          
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 289/319                            
#> 290/319 [dotplot_4_MOD_2]          
#> 291/319                            
#> 292/319 [dotplot_by_ori_2_MOD_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 293/319                            
#> 294/319 [dotplot_by_ori_3_MOD_2]   
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 295/319                            
#> 296/319 [dotplot_by_ori_4_MOD_2]   
#> 297/319                            
#> 298/319 [gene_info_1_MOD_2]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 299/319                            
#> 300/319 [gene_info_2_MOD_2]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 301/319                            
#> 302/319 [gene_info_3_MOD_2]        
#> 303/319                            
#> 304/319 [gene_info_4_MOD_2]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 305/319                            
#> 306/319 [level_2_MOD_2]            
#> 307/319                            
#> 308/319 [cell_annot_IA_1_MOD_2]    
#> 309/319                            
#> 310/319 [cell_annot_IA_2_MOD_2]    
#> 311/319                            
#> 312/319 [cell_annot_IA_3_MOD_2]    
#> 313/319                            
#> 314/319 [func_anno_MOD_2]          
#> 315/319                            
#> 316/319 [session_info]             
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 317/319                            
#> 318/319 [panel_setup_final]        
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> Warning: 'xfun::attr()' is deprecated.
#> Use 'xfun::attr2()' instead.
#> See help("Deprecated")
#> 319/319                            
#> output file: _main.knit.md
#> /usr/local/bin/pandoc +RTS -K512m -RTS _main.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _main.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/table-classes.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6O/file6c20796ddc40 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 2 --template /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --css style.css --mathjax --include-in-header /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpL90b6O/rmarkdown-str6c206087958b.html 
#> 
#> Output created: _book/index.html
#> |-- INFO :  Results have been copied to: /Users/puthier/gm_book