plotCellPatterns: plotCellPatterns This function provides a wrapper around...

In gofflab/glmpd: Identification of context-specific drivers of a pattern projection via GLM fitting.

Description

plotCellPatterns This function provides a wrapper around monocle3's plotting function to allow for clipping of color scales, to limit the effect of outliers on visualization. Implemented to plot continuous variables in pData that share common prefixes and unique appended ids... eg "pattern1" "pattern2" "patternZ"

Usage

plotCellPatterns(
  pattern_suffix,
  cds,
  pattern_prefix = NULL,
  red_method = "UMAP",
  do.clip = c(0, 1)
)

Arguments

pattern_suffix	A vector of names (or unique parts of names - used with pattern_prefix) of continuous values in pData to color cells by
cds	A monocle3 cell_data_set object
pattern_prefix	Used with pattern_suffix, if all variables to be plotted have a common prefix. only implemented like this to allow for lapply
red_method	Passed through monocle::plot_cells
do.clip	A vector of two numbers on the scale [0,1] indicating minimum and maximum percentiles at which to clip the color scale.

Value

Returns a plot (or list of plots) with cells colored by pattern weight

gofflab/glmpd documentation built on April 11, 2021, 6:38 a.m.