VlnPlot: Single cell violin plot

In nukappa/seurat_v2: 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, adjust.use = 1, size.use = 1, cols.use = NULL,
  group.by = "ident", y.log = F, ...)

Arguments

object	Seurat object
features.plot	Features to plot (gene expression, metrics, PC scores, anything that can be retreived by FetchData)
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
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)
y.log	plot T axis on log scale
...	additional parameters to pass to FetchData (for example, use.imputed, use.scaled, use.raw)

Value

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

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.