plotNovelty: Plot Novelty Score

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

Description

"Novelty" refers to log10 genes detected per count.

Usage

plotNovelty(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotNovelty(object, geom = c("ecdf",
  "ridgeline", "violin", "histogram", "boxplot"), interestingGroups, min = 0L,
  fill = NULL, trans = "identity", title = "genes per UMI (novelty)")

## S4 method for signature 'seurat'
plotNovelty(object, geom = c("ecdf", "ridgeline", "violin",
  "histogram", "boxplot"), interestingGroups, min = 0L, fill = NULL,
  trans = "identity", title = "genes per UMI (novelty)")

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.
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

See Also

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

Examples

# SingleCellExperiment ====
plotNovelty(cellranger_small)

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