Seurat (version 1.2.1)

genePlot: Scatter plot of single cell data

Description

Creates a scatter plot of two features (typically gene expression), across a set of single cells. Cells are colored by their identity class.

Usage

genePlot(object, gene1, gene2, cell.ids = NULL, col.use = NULL, pch.use = 16, cex.use = 1.5, use.imputed = FALSE, do.ident = FALSE, do.spline = FALSE, ...)

Arguments

object

Seurat object

gene1

First feature to plot. Typically gene expression but can also be metrics, PC scores, etc. - anything that can be retreived with fetch.data

gene2

Second feature to plot.

cell.ids

Cells to include on the scatter plot.

col.use

Colors to use for identity class plotting.

pch.use

Pch argument for plotting

cex.use

Cex argument for plotting

use.imputed

Use imputed values for gene expression (Default is FALSE)

do.ident

False by default. If TRUE,

do.spline

Add a spline (currently hardwired to df=4, to be improved)

...

Additional arguments to be passed to plot.

Value

No return, only graphical output