plotUMIsPerCell: Plot UMIs per Cell

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

Description

Plot the universal molecular identifiers (UMIs) per cell.

Usage

plotUMIsPerCell(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotUMIsPerCell(object, geom = c("ecdf",
  "ridgeline", "violin", "histogram", "boxplot"), interestingGroups, min = 0L,
  max = Inf, point = c("none", "inflection", "knee"), trans = "log10",
  color = NULL, fill = NULL, title = "UMIs per cell")

## S4 method for signature 'seurat'
plotUMIsPerCell(object, geom = c("ecdf", "ridgeline",
  "violin", "histogram", "boxplot"), interestingGroups, min = 0L, max = Inf,
  point = c("none", "inflection", "knee"), trans = "log10", color = NULL,
  fill = NULL, title = "UMIs 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.
point	Label either the "knee" or "inflection" points per sample. To disable, use "none". Requires geom = "ecdf".
trans	Name of the axis scale transformation to apply. See help("scale_x_continuous", "ggplot2") for more information.
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().
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, plotGenesPerCell, plotMitoRatio, plotMitoVsCoding, plotNovelty, plotQC, plotReadsPerCell, plotZerosVsDepth

Examples

# SingleCellExperiment ====
plotUMIsPerCell(cellranger_small, geom = "ecdf")
plotUMIsPerCell(cellranger_small, geom = "histogram")
plotUMIsPerCell(cellranger_small, geom = "ridgeline")
plotUMIsPerCell(cellranger_small, geom = "violin")
plotUMIsPerCell(cellranger_small, geom = "boxplot")

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