filter_data: filter_data: Filters cells/spots, genes, or samples

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

filter_data: Filters cells/spots, genes, or samples

Description

Filtering of spots/cells, genes or samples, as well as count-based filtering

Usage

filter_data(
  x = NULL,
  spot_minreads = 0,
  spot_maxreads = NULL,
  spot_mingenes = 0,
  spot_maxgenes = NULL,
  spot_minpct = 0,
  spot_maxpct = NULL,
  gene_minreads = 0,
  gene_maxreads = NULL,
  gene_minspots = 0,
  gene_maxspots = NULL,
  gene_minpct = 0,
  gene_maxpct = NULL,
  samples = NULL,
  rm_tissue = NULL,
  rm_spots = NULL,
  rm_genes = NULL,
  rm_genes_expr = NULL,
  spot_pct_expr = "^MT-"
)

Arguments

x	an STlist
spot_minreads	the minimum number of total reads for a spot to be retained
spot_maxreads	the maximum number of total reads for a spot to be retained
spot_mingenes	the minimum number of non-zero counts for a spot to be retained
spot_maxgenes	the maximum number of non-zero counts for a spot to be retained
spot_minpct	the minimum percentage of counts for features defined by spot_pct_expr for a spot to be retained.
spot_maxpct	the maximum percentage of counts for features defined by spot_pct_expr for a spot to be retained.
gene_minreads	the minimum number of total reads for a gene to be retained
gene_maxreads	the maximum number of total reads for a gene to be retained
gene_minspots	he minimum number of spots with non-zero counts for a gene to be retained
gene_maxspots	the maximum number of spots with non-zero counts for a gene to be retained
gene_minpct	the minimum percentage of spots with non-zero counts for a gene to be retained
gene_maxpct	the maximum percentage of spots with non-zero counts for a gene to be retained
samples	samples (as in names(x@counts)) to perform filtering.
rm_tissue	sample (as in names(x@counts)) to remove from STlist. Removes samples in x@counts, x@tr_counts, x@spatial_meta, x@gene_meta, and x@sample_meta
rm_spots	vector of spot/cell IDs to remove. Removes spots/cells in x@counts, x@tr_counts, and x@spatial_meta
rm_genes	vector of gene names to remove from STlist. Removes genes in x@counts, x@tr_counts, and x@gene_meta
rm_genes_expr	a regular expression that matches genes to remove. Removes genes in x@counts, x@tr_counts, and x@gene_meta
spot_pct_expr	a expression to use with spot_minpct and spot_maxpct. By default '^MT-'.

Details

This function provides options to filter elements in an STlist. It can remove cells/spots or genes based on raw counts (x@counts). Users can input an regular expression to query gene names and calculate percentages (for example % mtDNA genes). The function also can filter entire samples. Note that the function removes cells/spots, genes, and/or samples in the raw counts, transformed counts, spatial variables, gene variables, and sample metadata. Also note that the function filters in the following order:

1. Samples (rm_tissue)

2. Spots (rm_spots)

3. Genes (rm_genes)

4. Genes matching rm_genes_expr

5. Min and max counts

Value

an STlist containing the filtered data

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 <- filter_data(melanoma, spot_minreads=2000)

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