plotSigGene: plot signature genes

plotSigGeneR Documentation

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.