Seurat (version 2.0.0)

VariableGenePlot: View variable genes

Description

View variable genes

Usage

VariableGenePlot(object, do.text = TRUE, cex.use = 0.5,
  cex.text.use = 0.5, do.spike = FALSE, pch.use = 16, col.use = "black",
  spike.col.use = "red", plot.both = FALSE, do.contour = TRUE,
  contour.lwd = 3, contour.col = "white", contour.lty = 2,
  x.low.cutoff = 0.1, x.high.cutoff = 8, y.cutoff = 1,
  y.high.cutoff = Inf)

Arguments

object

Seurat object

do.text

Add text names of variable genes to plot (default is TRUE)

cex.use

Point size

cex.text.use

Text size

do.spike

FALSE by default. If TRUE, color all genes starting with ^ERCC a different color

pch.use

Pch value for points

col.use

Color to use

spike.col.use

if do.spike, color for spike-in genes

plot.both

Plot both the scaled and non-scaled graphs.

do.contour

Draw contour lines calculated based on all genes

contour.lwd

Contour line width

contour.col

Contour line color

contour.lty

Contour line type

x.low.cutoff

Bottom cutoff on x-axis for identifying variable genes

x.high.cutoff

Top cutoff on x-axis for identifying variable genes

y.cutoff

Bottom cutoff on y-axis for identifying variable genes

y.high.cutoff

Top cutoff on y-axis for identifying variable genes