vlnPlot: VlnPlot for the pathways

In guokai8/scGSVA: GSVA and UCell signature enrichment analysis for single cell RNA seq

VlnPlot for the pathways

Description

Draws a violin plot of single cell data (KEGG, GO)

Usage

vlnPlot(
  object,
  features,
  group_by = NULL,
  color = NULL,
  split.by = NULL,
  split.plot = FALSE,
  pt.size = 0,
  pt.shape = 19,
  nrow = NULL,
  ncol = NULL,
  basesize = 12
)

Arguments

object	A GSVA objectect or data.frame
features	A vector of features to plot
group_by	Name of one or more metadata columns to group (color) cells by
color	Colors to use for identity class plotting
split.by	Factor to split the groups by
split.plot	plot each group of the split violin plots by multiple or single violin shapes.
pt.size	Size of the points on the plot
pt.shape	If NULL, all points are circles (default)
nrow	Number of rows
ncol	Number of columns
basesize	base font size, given in pts.

Author(s)

Kai Guo

Examples

set.seed(123)
library(scGSVA)
data(pbmc_small)
hsko<-buildAnnot(species="human",keytype="SYMBOL",anntype="KEGG")
res<-scgsva(pbmc_small,hsko)
vlnPlot(res,features="Wnt.signaling.pathway")

guokai8/scGSVA documentation built on Nov. 15, 2024, 12:54 a.m.