plotDot: Plot Dot

In roryk/bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description

Plot Dot

Usage

## S4 method for signature 'SingleCellExperiment'
plotDot(object, genes, color = NULL,
  colMin = -2.5, colMax = 2.5, dotMin = 0L, dotScale = 6L,
  legend = TRUE)

## S4 method for signature 'seurat'
plotDot(object, genes, color = NULL, colMin = -2.5,
  colMax = 2.5, dotMin = 0L, dotScale = 6L, legend = TRUE)

Arguments

object	Object.
genes	Gene identifiers. Must match the rownames of the object.
color	Desired ggplot color scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().
colMin	Minimum scaled average expression threshold. Everything smaller will be set to this.
colMax	Maximum scaled average expression threshold. Everything larger will be set to this.
dotMin	The fraction of cells at which to draw the smallest dot. All cell groups with less than this expressing the given gene will have no dot drawn.
dotScale	Scale the size of the points, similar to cex.
legend	Include plot legend.

Value

ggplot.

Author(s)

Michael Steinbaugh

See Also

Modified version of Seurat::DotPlot().

Other Gene Expression Functions: plotGene, plotViolin

Examples

# seurat ====
object <- seurat_small
genes <- head(rownames(object))
plotDot(object, genes = genes)

roryk/bcbioSinglecell documentation built on May 27, 2019, 10:44 p.m.