pseudobulk_heatmap: pseudobulk_heatmap: Heatmap of pseudobulk samples

In spatialGE: Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

pseudobulk_heatmap: Heatmap of pseudobulk samples

Description

Generates a heatmap plot after computation of "pseudobulk" counts

Usage

pseudobulk_heatmap(
  x = NULL,
  color_pal = "muted",
  plot_meta = NULL,
  hm_display_genes = 30
)

Arguments

x	an STlist with pseudobulk counts in the ⁠@misc⁠ slot (generated by pseudobulk_samples)
color_pal	a string of a color palette from khroma or RColorBrewer, or a vector of color names or HEX values. Each color represents a category in the variable specified in plot_meta
plot_meta	a string indicating the name of the variable in the sample metadata to annotate heatmap columns
hm_display_genes	number of genes to display in heatmap, selected based on decreasing order of standard deviation across samples

Details

Generates a heatmap of transformed "pseudobulk" counts to help in initial data exploration of differences among samples. Each column in the heatmap represents a "pseudobulk" sample. Rows are genes, with the number of genes displayed controlled by the hm_display_genes argument. This function follows after usage of pseudobulk_samples.

Value

a ggplot object

Examples

# Using included melanoma example (Thrane et al.)
# Download example data set from spatialGE_Data
thrane_tmp = tempdir()
unlink(thrane_tmp, recursive=TRUE)
dir.create(thrane_tmp)
lk='https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
tryCatch({ # In case data is not available from network
  download.file(lk, destfile=paste0(thrane_tmp, '/', 'melanoma_thrane.zip'), mode='wb')
  #' zip_tmp = list.files(thrane_tmp, pattern='melanoma_thrane.zip$', full.names=TRUE)
  unzip(zipfile=zip_tmp, exdir=thrane_tmp)
  # Generate the file paths to be passed to the STlist function
  count_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
                            full.names=TRUE, pattern='counts')
  coord_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
                            full.names=TRUE, pattern='mapping')
  clin_file <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
                          full.names=TRUE, pattern='clinical')
  # Create STlist
  library('spatialGE')
  melanoma <- STlist(rnacounts=count_files,
                     spotcoords=coord_files,
                     samples=clin_file)
  melanoma <- pseudobulk_samples(melanoma)
  hm <- pseudobulk_heatmap(melanoma, plot_meta='BRAF_status', hm_display_genes=30)
}, error = function(e) {
  message("Could not run example. Are you connected to the internet?")
  return(NULL)
})

spatialGE documentation built on June 8, 2025, 11:10 a.m.