STplot: STplot: Plots of gene expression, cluster memberships, and...

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

STplot: Plots of gene expression, cluster memberships, and metadata in spatial context

Description

Generates a plot of the location of spots/cells within an spatial sample, and colors them according to gene expression levels or spot/cell-level metadata

Usage

STplot(
  x,
  samples = NULL,
  genes = NULL,
  plot_meta = NULL,
  ks = "dtc",
  ws = NULL,
  deepSplit = NULL,
  color_pal = NULL,
  data_type = "tr",
  ptsize = NULL,
  txsize = NULL
)

Arguments

x	an STlist
samples	a vector of numbers indicating the ST samples to plot, or their sample names. If vector of numbers, it follow the order of samples in names(x@counts). If NULL, the function plots all samples
genes	a vector of gene names or a named list of gene sets. In the latter case, the averaged expression of genes within the sets is plotted
plot_meta	a column name in x@spatial_meta to plot
ks	the k values to plot or 'dtc' to plot results from dynamicTreeCut clustering solutions. Requires previous analysis with STclust
ws	the spatial weights to plot samples if STclust was used
deepSplit	a logical or positive number indicating the deepSplit, if samples were analyzed with STclust
color_pal	a string of a color palette from khroma or RColorBrewer, or a vector with enough color names or HEX values
data_type	one of 'tr' or 'raw', to plot transformed or raw counts respectively
ptsize	a number specifying the size of the points. Passed to the size
txsize	a number controlling the size of the text in the plot title and legend title. Passed to the element_text aesthetic.

Details

The function takes an STlist and plots the cells or spots in their spatial context. The users can color the spots/cells according to the expression of selected genes, cluster memberships, or any spot/cell level metadata included in x@spatial_meta. The function also can average expression of gene sets.

Value

a list of plots

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 <- transform_data(melanoma)
  STplot(melanoma, gene='MLANA', samples='ST_mel1_rep2', ptsize=1)
}, 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.