supercell_VlnPlot: Violin plots

In SuperCell: Simplification of scRNA-Seq Data by Merging Together Similar Cells

Violin plots

Description

Violin plots (similar to VlnPlot with some changes for super-cells)

Usage

supercell_VlnPlot(
  ge,
  supercell_size = NULL,
  clusters,
  features = NULL,
  idents = NULL,
  color.use = NULL,
  pt.size = 0,
  pch = "o",
  y.max = NULL,
  y.min = NULL,
  same.y.lims = FALSE,
  adjust = 1,
  ncol = NULL,
  combine = TRUE,
  angle.text.y = 90,
  angle.text.x = 45
)

Arguments

ge	a gene expression matrix (ncol same as number of super-cells)
supercell_size	a vector with supercell size (ordered the same way as in ge)
clusters	a vector with clustering information (ordered the same way as in ge)
features	name of genes of for which gene expression is plotted
idents	idents (clusters) to plot (default all)
color.use	colors for idents
pt.size	point size (0 by default)
pch	shape of jitter dots
y.max	max of y axis
y.min	min of y axis
same.y.lims	same y axis for all plots
adjust	param of geom_violin
ncol	number of columns in combined plot
combine	combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot
angle.text.y	rotation of y text
angle.text.x	rotation of x text

Value

combined ggplot or list of ggplots if combine = TRUE

SuperCell documentation built on Oct. 25, 2024, 5:07 p.m.