ssc.plot.GeneDensity: plot gene expression density

In Japrin/sscVis: simpler single cell RNAseq data Visualization

plot gene expression density

Description

plot gene expression density

Usage

ssc.plot.GeneDensity(
  obj,
  out.prefix,
  gene.id,
  gene.symbol,
  assay.name = "norm_exprs",
  expT = c(0.3, 0.3),
  pallete.name = "heat",
  ann.txt.dis = 0.3,
  ann.txt.cex = 1.2,
  my.title = "",
  par.title = list(side = 3, cex = 1.8, line = -3, adj = 0.5)
)

Arguments

obj	object of SingleCellExperiment class
out.prefix	character; output prefix. required
gene.id	should be in rownames(obj); genes to plot
gene.symbol	should be in rowData(obj)[,"display.name"]; genes to plot
assay.name	character; which assay (default: "exprs")
expT	double; expression threshold of the genes. (default: c(0.3,0.3))
pallete.name	character; pallete to use. (default: "heat")
ann.txt.dis	double; adjust the position of the annotation text (default: 0.3)
ann.txt.cex	double; cex for annotation text (default: 1.2)
my.title	character; title of the figure (default: "")
par.title	list; parameters for drawing title by mtext (default: list(side=3,cex=1.8,line=-3,adj=0.5))

Details

make density plot of genes. Note, density estimation from ggplot2 is different (and not so 'effective' as that from ks::kde). One of gene.id and gene.symbol must be provided.

Japrin/sscVis documentation built on March 5, 2025, 10:23 a.m.