plotGenesPerCell: Plot Genes per Cell

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

Description

Plot Genes per Cell

Usage

plotGenesPerCell(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotGenesPerCell(object, geom = c("ecdf",
  "ridgeline", "violin", "histogram", "boxplot"), interestingGroups, min = 0L,
  max = Inf, trans = "log2", fill = NULL, title = "genes per cell")

## S4 method for signature 'seurat'
plotGenesPerCell(object, geom = c("ecdf", "ridgeline",
  "violin", "histogram", "boxplot"), interestingGroups, min = 0L, max = Inf,
  trans = "log2", fill = NULL, title = "genes per cell")

Arguments

object	Object.
...	Additional arguments.
geom	Plot type. Uses match.arg() and defaults to the first argument in the vector.
interestingGroups	Character vector of interesting groups. Must be formatted in camel case and intersect with sampleData() colnames.
min	Recommended minimum value cutoff.
max	Recommended maximum value cutoff.
trans	Name of the axis scale transformation to apply. See help("scale_x_continuous", "ggplot2") for more information.
fill	Desired ggplot fill 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_fill_manual().
title	Plot title.

Value

ggplot.

Author(s)

Michael Steinbaugh, Rory Kirchner

See Also

Other Quality Control Functions: barcodeRanksPerSample, filterCells, metrics, plotCellCounts, plotMitoRatio, plotMitoVsCoding, plotNovelty, plotQC, plotReadsPerCell, plotUMIsPerCell, plotZerosVsDepth

Examples

# SingleCellExperiment ====
plotGenesPerCell(cellranger_small)

WeiSong-bio/roryk-bcbioSinglecell documentation built on July 6, 2019, 12:03 a.m.