barPlotCellTypes {digitalDLSorteR}

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 deconvDDLSObj

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)