plotUMIsPerCell: Plot UMIs per Cell
In WeiSong-bio/roryk-bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description Usage Arguments Value Author(s) See Also Examples

Plot the universal molecular identifiers (UMIs) per cell.

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")

`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.

ggplot.

Michael Steinbaugh, Rory Kirchner

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

# 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")