barPlotCellTypes: Bar plot of deconvoluted cell type proportions in bulk...

In digitalDLSorteR: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning

Bar plot of deconvoluted cell type proportions in bulk RNA-Seq samples

Description

Bar plot of deconvoluted cell type proportions in bulk RNA-Seq samples.

Usage

barPlotCellTypes(
  data,
  colors = NULL,
  simplify = NULL,
  color.line = NA,
  x.label = "Bulk samples",
  rm.x.text = FALSE,
  title = "Results of deconvolution",
  legend.title = "Cell types",
  angle = 90,
  theme = NULL,
  ...
)

## S4 method for signature 'DigitalDLSorter'
barPlotCellTypes(
  data,
  colors = NULL,
  simplify = NULL,
  color.line = NA,
  x.label = "Bulk samples",
  rm.x.text = FALSE,
  title = "Results of deconvolution",
  legend.title = "Cell types",
  angle = 90,
  theme = NULL,
  name.data = NULL
)

## S4 method for signature 'ANY'
barPlotCellTypes(
  data,
  colors,
  color.line = NA,
  x.label = "Bulk samples",
  rm.x.text = FALSE,
  title = "Results of deconvolution",
  legend.title = "Cell types",
  angle = 90,
  theme = NULL
)

Arguments

data	DigitalDLSorter object with deconv.results slot or a data frame/matrix with cell types as columns and samples as rows.
colors	Vector of colors to be used.
simplify	Type of simplification performed during deconvolution. Can be simpli.set or simpli.maj (NULL by default). It is only for DigitalDLSorter objects.
color.line	Color of the border bars.
x.label	Label of x-axis.
rm.x.text	Logical value indicating whether to remove x-axis ticks (name of samples).
title	Title of the plot.
legend.title	Title of the legend plot.
angle	Angle of text ticks.
theme	ggplot2 theme.
...	Other arguments for specific methods.
name.data	If a DigitalDLSorter is given, name of the element that stores the results in the deconv.results slot.

Value

A ggplot object with the provided cell proportions represented as a bar plot.

See Also

deconvDigitalDLSorter deconvDigitalDLSorterObj

Examples

# matrix of simulated proportions (same estructure as deconvolution results)
deconvResults <- gtools::rdirichlet(n = 20, alpha = c(1, 1, 1, 0.5, 0.1))
colnames(deconvResults) <- paste("CellType", seq(ncol(deconvResults)))
rownames(deconvResults) <- paste("BulkSample", seq(nrow(deconvResults)))
barPlotCellTypes(deconvResults)

# Using a DigitalDLSorter object
DDLS <- DigitalDLSorter(deconv.results = list(Example = deconvResults))
barPlotCellTypes(DDLS)

digitalDLSorteR documentation built on Oct. 5, 2022, 9:05 a.m.