Seurat (version 2.3.4)

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, ident.include = NULL, nCol = NULL,
  do.sort = FALSE, y.max = NULL, same.y.lims = FALSE, size.x.use = 16,
  size.y.use = 16, size.title.use = 20, adjust.use = 1,
  point.size.use = 1, cols.use = NULL, group.by = NULL, y.log = FALSE,
  x.lab.rot = FALSE, y.lab.rot = FALSE, legend.position = "right",
  single.legend = TRUE, remove.legend = FALSE, do.return = FALSE,
  return.plotlist = FALSE, ...)

Arguments

object

Seurat object

features.plot

Features to plot (gene expression, metrics, PC scores, anything that can be retreived by FetchData)

ident.include

Which classes to include in the plot (default is all)

nCol

Number of columns if multiple plots are displayed

do.sort

Sort identity classes (on the x-axis) by the average expression of the attribute being potted

y.max

Maximum y axis value

same.y.lims

Set all the y-axis limits to the same values

size.x.use

X axis title font size

size.y.use

Y axis title font size

size.title.use

Main title font size

adjust.use

Adjust parameter for geom_violin

point.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 Y axis on log scale

x.lab.rot

Rotate x-axis labels

y.lab.rot

Rotate y-axis labels

legend.position

Position the legend for the plot

single.legend

Consolidate legend the legend for all plots

remove.legend

Remove the legend from the plot

do.return

Return a ggplot2 object (default : FALSE)

return.plotlist

Return the list of individual plots instead of compiled plot.

…

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.

Examples

# NOT RUN {
VlnPlot(object = pbmc_small, features.plot = 'PC1')

# }