gene_interpolation: gene_interpolation: Spatial interpolation of gene expression

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

gene_interpolation: Spatial interpolation of gene expression

Description

Performs spatial interpolation ("kriging") of transformed gene counts

Usage

gene_interpolation(
  x = NULL,
  genes = "top",
  top_n = 10,
  samples = NULL,
  cores = NULL
)

Arguments

x	an STlist with transformed RNA counts
genes	a vector of gene names or 'top'. If 'top' (default), interpolation of the 10 genes (top_n default) with highest standard deviation in each ST sample is estimated.
top_n	an integer indicating how many top genes to perform interpolation. Default is 10.
samples	the spatial samples for which interpolations will be performed. If NULL (Default), all samples are interpolated.
cores	integer indicating the number of cores to use during parallelization. If NULL, the function uses half of the available cores at a maximum. The parallelization uses parallel::mclapply and works only in Unix systems.

Details

This function takes an STlist and a vector of gene names and generates spatial interpolation of gene expression values via "kriging". If genes='top', then the 10 genes (default) with the highest standard deviation for each ST sample are interpolated. The resulting interpolations can be visualized via the STplot_interpolation function

Value

x a STlist including spatial interpolations.

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[c(1,2)],
                   spotcoords=coord_files[c(1,2)],
                   samples=clin_file) # Only first two samples
melanoma <- transform_data(melanoma)
melanoma <- gene_interpolation(melanoma, genes=c('MLANA', 'COL1A1'), samples='ST_mel1_rep2')
kp = STplot_interpolation(melanoma, genes=c('MLANA', 'COL1A1'))
ggpubr::ggarrange(plotlist=kp)

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