plotUMIsPerCell: Plot UMIs per Cell

Description Usage Arguments Value Author(s) See Also Examples

Description

Plot the universal molecular identifiers (UMIs) per cell.

Usage

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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

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# 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")

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