plotCountsPerCell: Plot counts per cell

In acidgenomics/r-acidplots: Acid Genomics Plot Functions and Themes

Plot counts per cell

Description

Plot the disambiguated counts per cell.

Usage

plotCountsPerCell(object, ...)

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

Arguments

object	Object.
geom	character(1). Plot type. Uses match.arg() internally and defaults to the first argument in the character vector.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
min	numeric(1). Recommended minimum value cutoff.
max	numeric(1). Recommended maximum value cutoff.
point	character(1). Label either the knee or inflection points per sample. Requires geom = "ecdf".
trans	character(1). Name of the axis scale transformation to apply. For more information: help(topic = "scale_x_continuous", package = "ggplot2")
title	character(1). Title.
...	Additional arguments.

Details

"Counts" refer to universal molecular identifier (UMI) counts for droplet-based scRNA-seq data.

Value

ggplot.

Note

Updated 2023-08-11.

Author(s)

Michael Steinbaugh, Rory Kirchner

See Also

plotCountsVsFeatures().

Examples

data(SingleCellExperiment_splatter, package = "AcidTest")

## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
plotCountsPerCell(object, geom = "violin")
plotCountsPerCell(object, geom = "ridgeline")
plotCountsPerCell(object, geom = "ecdf")
plotCountsPerCell(object, geom = "histogram")
plotCountsPerCell(object, geom = "boxplot")

acidgenomics/r-acidplots documentation built on March 30, 2024, 10:16 p.m.