plotGeneExpression: A Seurat wrapper function for plotting gene expression using...

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

A Seurat wrapper function for plotting gene expression using violin plot, dot plot or bar plot

Description

This function create a Seurat object from an input CellChat object, and then plot gene expression distribution using a modified violin plot or dot plot based on Seurat's function or a bar plot. Please check StackedVlnPlot,dotPlot and barPlotfor detailed description of the arguments.

Usage

plotGeneExpression(
  object,
  features = NULL,
  signaling = NULL,
  enriched.only = TRUE,
  type = c("violin", "dot", "bar"),
  color.use = NULL,
  group.by = NULL,
  ...
)

Arguments

object	CellChat object
features	Features to plot gene expression
signaling	a char vector containing signaling pathway names for searching
enriched.only	whether only return the identified enriched signaling genes in the database. Default = TRUE, returning the significantly enriched signaling interactions
type	violin plot or dot plot
color.use	defining the color for each cell group
group.by	Name of one metadata columns to group (color) cells. Default is the defined cell groups in CellChat object
...	other arguments passing to either VlnPlot or DotPlot from Seurat package

Details

USER can extract the signaling genes related to the inferred L-R pairs or signaling pathway using extractEnrichedLR, and then plot gene expression using Seurat package.

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