plot_gene_two_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 two discrete regions based on high or low explanatory variable values. 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 two discrete regions based on high or low explanatory variable values. Bold points represent expressed, whereas unbold points represent pixels not expressing the gene.

Usage

plot_gene_two_regions(
  myRCTD,
  gene,
  cell_type,
  min_UMI = 200,
  expr.thresh = 0,
  exvar_thresh = 0.5
)

Arguments

myRCTD	RCTD object containing de_results, after running CSIDE
gene	gene to be plotted
cell_type	cell_type to be plotted (only single cell type pixels)
min_UMI	(default 200) minimum UMI for pixels that are included
expr.thresh	(default 0) the minimum expression threshold to clear to be considered to be expressed
exvar_thresh	threshold of the explanatory variable in order for points to be sorted into the two regions

Value

gene expression plot

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