plot_heatmap — plot_heatmap • scigenex

Plot the observed and simulated distance with the Kth nearest neighbors.

plot_heatmap(
  object,
  center = TRUE,
  ceil = 1,
  floor = -1,
  cell_clusters = NULL,
  show_dendro = TRUE,
  use_top_genes = FALSE,
  interactive = TRUE,
  name = NULL,
  xlab = NULL,
  ylab = NULL,
  colorbar_name = "Exp. level",
  show_legend = TRUE,
  colors = colors_for_gradient("Ju1"),
  colors_cell_clusters = NULL,
  row_labels = TRUE,
  col_labels = FALSE,
  label_size = 10,
  line_size_vertical = 3,
  line_size_horizontal = 3,
  link = c("average", "complete", "single", "ward.D", "ward.D2", "mcquitty")
)

Arguments

object: A ClusterSet object.
center: A logical to indicate whether to center row..
ceil: A value for ceiling (NULL for no ceiling). Ceiling is performed centering.
floor: A value for flooring (NULL for no flooring). Flooring is performed after centering.
cell_clusters: A vector of cell clusters with cell barcodes as names.
show_dendro: A logical to indicate whether to show column dendrogram.
use_top_genes: A logical to indicate whether to use highly similar genes in the slot top_genes of ClusterSet.
interactive: A logical to indicate if the heatmap should be interactive.
name: A title for the heatmap (if interactive is TRUE).
xlab: A title for the x axis (if interactive is TRUE).
ylab: A title for the y axis (if interactive is TRUE).
colorbar_name: A title for the colorbar.
show_legend: A logical to indicate whether to show colorbar.
colors: A vector of colors.
colors_cell_clusters: A named vector of colors for cell identity annotations.
row_labels: A logical to indicate whether to show row labels.
col_labels: A logical to indicate whether to show col labels.
label_size: A value for label font size.
line_size_vertical: An integer for the size of horizontal white line which separate gene clusters.
line_size_horizontal: An integer for the size of vertical white line which separate cell clusters.
link: The aggloremative criterion for hierarchical clustering. One of "average", "complete" or "single". Default to average.

Value

Iheatmap-class object.

Examples

library(Seurat)
# Set verbosity to 1 to display info messages only.
set_verbosity(1)

# Load datasets
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. 

# Plot heatmap of 'top genes' of all gene clusters
pbmc3k_medium_clusters <- top_genes(pbmc3k_medium_clusters)
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 6. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 7. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 8. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 9. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 10. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 11. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 12. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 13. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 14. All genes will be used. 
#> |-- INFO :  Number of top genes is greater than the number of genes in cluster 15. All genes will be used. 
#> |-- INFO :  Results are stored in top_genes slot of ClusterSet object. 
plot_heatmap(pbmc3k_medium_clusters, use_top_genes=TRUE)
#> |-- INFO :  cell_clusters is not NULL. Setting show_dendro to FALSE 
#> |-- INFO :  Centering matrix. 
#> |-- INFO :  Ceiling matrix. 
#> |-- INFO :  Flooring matrix. 
#> |-- INFO :  Ordering cells/columns using hierarchical clustering. 
#> |-- INFO :  Only top genes will be used. 
#> |-- INFO :  Plotting heatmap. 
#> |-- INFO :  Plot is interactive... 

# Plot heatmap of gene cluster 1
plot_heatmap(pbmc3k_medium_clusters[1,]) 
#> |-- INFO :  cell_clusters is not NULL. Setting show_dendro to FALSE 
#> |-- INFO :  Centering matrix. 
#> |-- INFO :  Ceiling matrix. 
#> |-- INFO :  Flooring matrix. 
#> |-- INFO :  Ordering cells/columns using hierarchical clustering. 
#> |-- INFO :  Plotting heatmap. 
#> |-- INFO :  Plot is interactive... 

# Plot heatmap of gene cluster 1 and 3
plot_heatmap(pbmc3k_medium_clusters[c(1,3),])  
#> |-- INFO :  cell_clusters is not NULL. Setting show_dendro to FALSE 
#> |-- INFO :  Centering matrix. 
#> |-- INFO :  Ceiling matrix. 
#> |-- INFO :  Flooring matrix. 
#> |-- INFO :  Ordering cells/columns using hierarchical clustering. 
#> |-- INFO :  Plotting heatmap. 
#> |-- INFO :  Plot is interactive... 

# Plot heatmap of 'top genes' of all gene clusters
# with cell ordered according to Seurat results
plot_heatmap(pbmc3k_medium_clusters, use_top_genes=TRUE, cell_clusters=Seurat::Idents(pbmc3k_medium))
#> |-- INFO :  Extracting cell identity. 
#> |-- INFO :  Centering matrix. 
#> |-- INFO :  Ceiling matrix. 
#> |-- INFO :  Flooring matrix. 
#> |-- INFO :  Only top genes will be used. 
#> |-- INFO :  Plotting heatmap. 
#> |-- INFO :  Plot is interactive... 

# Plot heatmap of 'top genes' of all gene clusters
# with cell ordered according to Seurat results
# (non interactive version)
plot_heatmap(pbmc3k_medium_clusters, use_top_genes=TRUE, 
             cell_clusters=Seurat::Idents(pbmc3k_medium),
             interactive=FALSE, label_size = 2)
#> |-- INFO :  Extracting cell identity. 
#> |-- INFO :  Centering matrix. 
#> |-- INFO :  Ceiling matrix. 
#> |-- INFO :  Flooring matrix. 
#> |-- INFO :  Only top genes will be used. 
#> |-- INFO :  Plotting heatmap.