vlnPlot: Single cell violin plot

In paodan/studySeu: Seurat : R toolkit for single cell genomics

Description

Draws a violin plot of single cell data (gene expression, metrics, PC scores, etc.)

Usage

vlnPlot(object, features.plot, nCol = NULL, ylab.max = 12, do.ret = TRUE,
  do.sort = FALSE, size.x.use = 16, size.y.use = 16,
  size.title.use = 20, use.imputed = FALSE, adjust.use = 1,
  size.use = 1, cols.use = NULL, group.by = "ident")

Arguments

object	Seurat object
features.plot	Features to plot (gene expression, metrics, PC scores, anything that can be retreived by fetch.data)
nCol	Number of columns if multiple plots are displayed
ylab.max	Maximum ylab value
do.ret	FALSE by default. If TRUE, returns a list of ggplot objects.
do.sort	Sort identity classes (on the x-axis) by the average expression of the attribute being potted
size.x.use	X axis font size
size.y.use	Y axis font size
size.title.use	Title font size
use.imputed	Use imputed values for gene expression (default is FALSE)
adjust.use	Adjust parameter for geom_violin
size.use	Point size for geom_violin
cols.use	Colors to use for plotting
group.by	Group (color) cells in different ways (for example, orig.ident)

Value

By default, no return, only graphical output. If do.return=TRUE, returns a list of ggplot objects.

paodan/studySeu documentation built on May 23, 2019, 3:06 p.m.