plotQuantileHeatmap: Quantile heatmap

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

Quantile heatmap

Description

Quantile heatmap

Usage

plotQuantileHeatmap(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotQuantileHeatmap(object, ...)

## S4 method for signature 'SummarizedExperiment'
plotQuantileHeatmap(
  object,
  assay = 1L,
  interestingGroups = NULL,
  n = 10L,
  clusterRows = TRUE,
  clusterCols = TRUE,
  showRownames = isTRUE(nrow(object) <= 30L),
  showColnames = TRUE,
  treeheightRow = 50L,
  treeheightCol = 50L,
  color = getOption(x = "acid.heatmap.quantile.color", default = viridis::magma),
  legendColor = getOption(x = "acid.heatmap.legend.color", default =
    AcidPlots::synesthesia),
  legend = FALSE,
  borderColor = NULL,
  title = NULL,
  convertGenesToSymbols = showRownames,
  ...
)

Arguments

object	Object.
...	Additional arguments.
assay	vector(1). Assay name or index position.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
n	integer(1). The number of quantile breaks to create.
clusterRows, clusterCols	logical(1). Arrange with hierarchical clustering.
showRownames, showColnames	logical(1). Show row or column names.
treeheightRow, treeheightCol	integer(1). Size of the row and column dendrograms. Use 0 to disable.
color	function, character, or NULL. Hexadecimal color function or values to use for plot. We generally recommend these hexadecimal functions from the viridis package, in addition to our synesthesia() palette: viridis::viridis(). viridis::inferno(). viridis::magma(). viridis::plasma(). Alternatively, colors can be defined manually using hexadecimal values (e.g. c("#FF0000", "#0000FF")), but this is not generally recommended. Refer to the RColorBrewer package for hexadecimal color palettes that may be suitable. If set NULL, will use the default pheatmap colors.
legendColor	function or NULL. Hexadecimal color function to use for legend labels. Note that hexadecimal values are not supported. If set NULL, will use the default pheatmap colors.
legend	logical(1). Show the color legend.
borderColor	character(1) or NULL. Border color.
title	character(1). Title.
convertGenesToSymbols	logical(1). Attempt to automatically convert gene identifiers to gene symbols. Only applies when object contains mappings defined in rowRanges.

Value

Plot.

Note

Updated 2022-03-07.

Examples

data(
    RangedSummarizedExperiment,
    SingleCellExperiment_splatter,
    package = "AcidTest"
)

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
plotQuantileHeatmap(object)

## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
plotQuantileHeatmap(object)

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