plotSigGene: plot signature genes

In Japrin/sscClust: simpler single cell RNAseq data clustering

plot signature genes

Description

plot signature genes

Usage

plotSigGene(
  obj.list,
  gene.core.tb,
  out.prefix,
  assay.name = "exprs",
  adjB = NULL,
  meta.cluster = NULL,
  meta.info.tb = NULL,
  meta.col = "metaCluster",
  p.ncol = 2,
  pdf.width = NULL,
  pdf.height = NULL,
  verbose = F,
  ptype = "heatmap",
  ncores = 16,
  ...
)

Arguments

obj.list	object; named list of object of singleCellExperiment class
gene.core.tb	data.frame; signature genes
out.prefix	character; output prefix
assay.name	character; which assay (default: "exprs")
adjB	character; batch column of the colData(obj). (default: NULL)
meta.cluster	character; (default: NULL)
meta.info.tb	data.frame; cell information table (default: NULL)
meta.col	character; column in meta.info.tb, by which to group cells (default: "meta.cluster")
p.ncol	integer; number of columns in the violin plot (default: 2)
pdf.width	double; width of the output plot (default: NULL)
pdf.height	double; height of the output plot (default: NULL)
verbose	logical; (default: FALSE)
ptype	character; (default: "heatmap")
ncores	integer; number of CPU to used (default: 16)
...	parameters passed to plotting methods

Details

make some plot(s) of signature genes

Japrin/sscClust documentation built on May 23, 2024, 7:12 a.m.