DotPlot: Dot plot visualization

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

Description

Intuitive way of visualizing how gene expression changes across different identity classes (clusters). The size of the dot encodes the percentage of cells within a class, while the color encodes the AverageExpression level of 'expressing' cells (blue is high).

Usage

DotPlot(object, genes.plot, cols.use = c("lightgrey", "blue"),
  col.min = -2.5, col.max = 2.5, dot.min = 0, dot.scale = 6, group.by,
  plot.legend = FALSE, do.return = FALSE, x.lab.rot = FALSE)

Arguments

object	Seurat object
genes.plot	Input vector of genes
cols.use	colors to plot
col.min	Minimum scaled average expression threshold (everything smaller will be set to this)
col.max	Maximum scaled average expression threshold (everything larger will be set to this)
dot.min	The fraction of cells at which to draw the smallest dot (default is 0.05). All cell groups with less than this expressing the given gene will have no dot drawn.
dot.scale	Scale the size of the points, similar to cex
group.by	Factor to group the cells by
plot.legend	plots the legends
do.return	Return ggplot2 object
x.lab.rot	Rotate x-axis labels

Value

default, no return, only graphical output. If do.return=TRUE, returns a ggplot2 object

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