plotMitoRatio: Plot Mitochondrial Transcript Abundance

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

Description

Plot Mitochondrial Transcript Abundance

Usage

plotMitoRatio(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotMitoRatio(object, geom = c("ecdf",
  "ridgeline", "violin", "histogram", "boxplot"), interestingGroups, max = 1L,
  fill = NULL, trans = "sqrt", title = "mito ratio")

## S4 method for signature 'seurat'
plotMitoRatio(object, geom = c("ecdf", "ridgeline",
  "violin", "histogram", "boxplot"), interestingGroups, max = 1L,
  fill = NULL, trans = "sqrt", title = "mito ratio")

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.
max	Recommended maximum value cutoff.
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().
trans	Name of the axis scale transformation to apply. See help("scale_x_continuous", "ggplot2") for more information.
title	Plot title.

Value

ggplot.

Author(s)

Michael Steinbaugh, Rory Kirchner

See Also

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

Examples

# SingleCellExperiment ====
plotMitoRatio(cellranger_small)

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