JoyPlot: Single cell joy plot

In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

Description

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

Usage

JoyPlot(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, 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
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.

mayer-lab/SeuratForMayer2018 documentation built on May 25, 2019, 9:34 p.m.