pathHeatmap: To plot a heatmap of those differentially enriched pathways...

In yingyonghui/CommPath:

To plot a heatmap of those differentially enriched pathways for each cluster

Description

To plot a heatmap of those differentially enriched pathways for each cluster

Usage

pathHeatmap(
  object,
  acti.path.dat = NULL,
  top.n.pathway = 10,
  path.order = "P.val.adj",
  col = NULL,
  cell.aver = FALSE,
  cell.label.size = NULL,
  cell.label.angle = 45,
  pathway.label.size = NULL,
  scale = TRUE,
  truncation = 1.5,
  show.legend = TRUE
)

Arguments

object	CommPath object
acti.path.dat	Data frame of differential enrichment test result from diffAllPath; if NULL, diffAllPath would be run to get the acti.path.dat
top.n.pathway	Show the heatmap of top n most significant pathways
path.order	Sort criteria used to select the top n pathways, either 'P.val' or 'P.val.adj', which represent the original and adjusted p values, or 'diff' which represents the mean (in t test) or median (in wilcox test) difference
col	Vector of colors used to generate a series of gradient colors to show the enrichment score of pathways; provide a vector containing at least two colors
cell.aver	Whether to display averaged pathway enrichment scores among cells from the same clusters or to display scores for all cells; default is FALSE, which means to display scores for all cells
cell.label.size	Text size of the label of cell types
cell.label.angle	Rotation angle of the label of cell types
pathway.label.size	Text size of the label of pathways
scale	Whether to scale the enrichment sorces matrix among cells or not; default is TRUE
truncation	Truncation fold value; scores > (the third quartiles + truncation * interquartile range) and scores < (the first quartiles - truncation * interquartile range) will be adjusted; either a value to indicate the specific truncation value or 'none' to indicate no truncation; default is 1.5
show.legend	Whether to show the legend or not; default is FALSE

Value

Heatmap plot showing the top enriched patways in each cluster

yingyonghui/CommPath documentation built on June 15, 2025, 6:29 a.m.