plotGenesDetected: Plot Genes Detected

Description Usage Arguments Value Examples

Description

Plot Genes Detected

Usage

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## S4 method for signature 'SummarizedExperiment'
plotGenesDetected(object, assay = 1L,
  interestingGroups = NULL, limit = 0L, minCounts = 1L,
  fill = getOption("basejump.discrete.fill", NULL),
  flip = getOption("basejump.flip", TRUE), title = "genes detected")

## S4 method for signature 'SingleCellExperiment'
plotGenesDetected(object, assay = 1L,
  interestingGroups = NULL, limit = 0L, minCounts = 1L,
  fill = getOption("basejump.discrete.fill", NULL),
  flip = getOption("basejump.flip", TRUE), title = "genes detected")

Arguments

object

Object.

assay

scalar. Name or index of count matrix slotted in SummarizedExperiment::assays(). When passing in a string, the name must be defined in SummarizedExperiment::assayNames().

interestingGroups

character or NULL. Groups of interest that define the samples. If left unset, defaults to sampleName.

limit

scalar numeric. Threshold to denote on the plot, using a dashed line.

minCounts

scalar integer. Minimum number of counts per gene in the count matrix.

fill

ggproto/ScaleDiscrete or NULL. Desired ggplot2 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(). To set the discrete fill palette globally, use options(bcbio.discrete.fill = scale_fill_viridis_d()).

flip

boolean. Flip x and y axes. Recommended for plots containing many samples.

title

string or NULL. Plot title.

Value

ggplot.

Examples

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data(rse, sce, package = "basejump.data")
plotGenesDetected(rse)
plotGenesDetected(sce)

steinbaugh/basejump.plots documentation built on Nov. 5, 2018, 10:36 p.m.