pseudobulk_dim_plot: pseudobulk_dim_plot: Plot PCA of pseudobulk samples

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

pseudobulk_dim_plot: Plot PCA of pseudobulk samples

Description

Generates a PCA plot after computation of "pseudobulk" counts

Usage

pseudobulk_dim_plot(
  x = NULL,
  color_pal = "muted",
  plot_meta = NULL,
  dim = "pca",
  pcx = 1,
  pcy = 2,
  ptsize = 5
)

Arguments

x	an STlist with pseudobulk PCA results 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 color points in the PCA plot
dim	one of umap or pca. The dimension reduction to plot
pcx	integer indicating the principal component to plot in the x axis
pcy	integer indicating the principal component to plot in the y axis
ptsize	the size of the points in the PCA plot. Passed to the size aesthetic from ggplot2

Details

Generates a Principal Components Analysis plot to help in initial data exploration of differences among samples. The points in the plot represent "pseudobulk" samples. 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='
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, cores=2)
melanoma <- pseudobulk_samples(melanoma)
pseudobulk_dim_plot(melanoma, plot_meta='patient')

FridleyLab/spatialGE documentation built on April 14, 2025, 9:37 a.m.