plotSCEBatchFeatureMean: Plot mean feature value in each batch of a...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Plot mean feature value in each batch of a SingleCellExperiment object

Description

Plot mean feature value in each batch of a SingleCellExperiment object

Usage

plotSCEBatchFeatureMean(
  inSCE,
  useAssay = NULL,
  useReddim = NULL,
  useAltExp = NULL,
  batch = "batch",
  xlab = "batch",
  ylab = "Feature Mean",
  ...
)

Arguments

inSCE	SingleCellExperiment inherited object.
useAssay	A single character. The name of the assay that stores the value to plot. For useReddim and useAltExp also. Default NULL.
useReddim	A single character. The name of the dimension reduced matrix that stores the value to plot. Default NULL.
useAltExp	A single character. The name of the alternative experiment that stores an assay of the value to plot. Default NULL.
batch	A single character. The name of batch annotation column in colData(inSCE). Default "batch".
xlab	label for x-axis. Default "batch".
ylab	label for y-axis. Default "Feature Mean".
...	Additional arguments passed to .ggViolin.

Value

ggplot

Examples

data('sceBatches', package = 'singleCellTK')
plotSCEBatchFeatureMean(sceBatches, useAssay = "counts")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.