computeEnrichmentScore: Compute and visualize the enrichment score of ligand-receptor...

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

Compute and visualize the enrichment score of ligand-receptor pairs in one condition compared to another condition

Description

Compute and visualize the enrichment score of ligand-receptor pairs in one condition compared to another condition

Usage

computeEnrichmentScore(
  df,
  measure = c("ligand", "signaling", "LR-pair"),
  species = c("mouse", "human"),
  color.use = NULL,
  color.name = "Dark2",
  n.color = 8,
  scale = c(4, 0.8),
  min.freq = 0,
  max.words = 200,
  random.order = FALSE,
  rot.per = 0,
  return.data = FALSE,
  seed = 1,
  ...
)

Arguments

df	a dataframe
measure	compute the enrichment score in terms of "ligand", "signaling",or "LR-pair"
species	a vector giving the groups of different datasets to define colors of the bar plot. Default: only one group and a single color
color.use	defining the color for each group of datasets
color.name	the color names in RColorBrewer::brewer.pal
n.color	the number of colors
scale	A vector of length 2 indicating the range of the size of the words.
min.freq	words with frequency below min.freq will not be plotted
max.words	Maximum number of words to be plotted. least frequent terms dropped
random.order	plot words in random order. If false, they will be plotted in decreasing frequency
rot.per	proportion words with 90 degree rotation
return.data	whether return the data frame for plotting wordcloud
seed	set a seed
...	Other parameters passing to wordcloud::wordcloud

Value

A ggplot object

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.