spatialGE (version 1.2.2)

gene_interpolation: 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,
  verbose = TRUE
)

Value

x a STlist including spatial interpolations.

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.

verbose

either logical or an integer (0, 1, or 2) to increase verbosity.

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

Examples

# \donttest{
# 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)
  melanoma <- gene_interpolation(melanoma, genes=c('MLANA', 'COL1A1'), samples='ST_mel1_rep2')
  kp = STplot_interpolation(melanoma, genes=c('MLANA', 'COL1A1'))
  ggpubr::ggarrange(plotlist=kp)
}, error = function(e) {
  message("Could not run example. Are you connected to the internet?")
  return(NULL)
})
# }