Create a report from a ClusterSet and Seurat object.

cluster_set_report(
  clusterset_object = NULL,
  seurat_object = NULL,
  file_path = NULL,
  force = FALSE,
  report_title = "Scigenex_report",
  report_author = "Unknown",
  heatmap_colors = colors_for_gradient("Ju1"),
  heatmap_color_ident = NULL,
  coord_flip = TRUE,
  pt_size = 2.75,
  go_info = c("ID", "Description", "GeneRatio", "pvalue", "qvalue", "Count"),
  verbosity = 1,
  pandoc_heap_size = "512m",
  report_id = rlang::hash(clusterset_object)
)

Arguments

clusterset_object: The ClusterSet object.
seurat_object: The Seurat object.
file_path: A file path where to store the report (html extension).
force: Whether to force erase output file.
report_title: A title for the report.
report_author: Names of report authors.
heatmap_colors: Colors for the heatmap gradient.
heatmap_color_ident: Colors for cell classes.
coord_flip: Whether to flip spatial coordinates.
pt_size: Size of the spots.
go_info: Info about GO stats. Should be from the list: "ONTOLOGY", "ID", "Description", "GeneRatio", "BgRatio", "pvalue", "p.adjust", "qvalue", "geneID", "Count"
verbosity: The verbosity level (0-3, defaut to 1.)
pandoc_heap_size: Fix the maximum memory used by pandoc. See https://pandoc.org/MANUAL.html.
report_id: Used to label code chunks.

Examples

# Load datasets
set_verbosity(3)
library(Seurat)
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_clusters_2 has been loaded. 
load_example_dataset("7870305/files/lymph_node_tiny_2")
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_2 has been loaded. 
# Create a report
cluster_set_report(clusterset_object = lymph_node_tiny_clusters_2[1,],
                   seurat_object=lymph_node_tiny_2,
                   pt_size=6)
#> |-- DEBUG :  Checking ClusterSet format. 
#> |-- DEBUG :  Report ID is : e5cde0b97ddfd882ccff69e313ef025a 
#> |-- INFO :  Preparing report. 
#> |-- INFO :  Dumping dataset 
#> |-- INFO :  Writing report into /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmp7s9US9/scigenex_report436e61e79eed.Rmd 
#> |-- INFO :  Rmd file written at : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmp7s9US9/scigenex_report436e61e79eed.Rmd 
#> |-- INFO :  Rendering report. 
#> |-- INFO :  Creating report at : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmp7s9US9/scigenex_report436e61e79eed.html