plot_gene_regions: Makes a spatial plot of gene expression for a particular gene...

In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

Makes a spatial plot of gene expression for a particular gene This plot is colored by several discrete regions based on a categorical design matrix. Bold points represent expressed, whereas unbold points represent pixels not expressing the gene.

Description

Makes a spatial plot of gene expression for a particular gene This plot is colored by several discrete regions based on a categorical design matrix. Bold points represent expressed, whereas unbold points represent pixels not expressing the gene.

Usage

plot_gene_regions(
  myRCTD,
  cell_type,
  gene,
  pixel_weight_thresh = 0.8,
  expr_thresh = 0
)

Arguments

myRCTD	RCTD object containing de_results, after running CSIDE
cell_type	cell_type to be plotted (only single cell type pixels)
gene	gene to be plotted
pixel_weight_thresh	(default 0.8) minimum cell type weight for pixels that are included
expr_thresh	(default 0) the minimum expression threshold to clear to be considered to be expressed

Value

gene expression plot

dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.