SuperCell (version 1.1)

supercell_VlnPlot: 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
)

Value

combined ggplot or list of ggplots if combine = TRUE

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