Seurat (version 1.4.0)

VlnPlot: Single cell violin plot

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.