plotCorrelationHeatmap: Correlation heatmap

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

Correlation heatmap

Description

Correlation heatmap

Usage

plotCorrelationHeatmap(object, ...)

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

## S4 method for signature 'SummarizedExperiment'
plotCorrelationHeatmap(
  object,
  assay = 1L,
  interestingGroups = NULL,
  method = c("pearson", "kendall", "spearman"),
  clusteringMethod = "ward.D2",
  showRownames = TRUE,
  showColnames = TRUE,
  treeheightRow = 0L,
  treeheightCol = 50L,
  color = getOption(x = "acid.heatmap.correlation.color", default = viridis::magma),
  legendColor = getOption(x = "acid.heatmap.legend.color", default =
    AcidPlots::synesthesia),
  borderColor = NULL,
  title = TRUE,
  ...
)

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.
method	character(1). Correlation coefficient (or covariance) method to be computed. Defaults to pearson, but spearman or kendall can also be used. Refer to cor() documentation for details.
clusteringMethod	character(1). Clustering method. Accepts the same values as hclust().
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.
borderColor	character(1) or NULL. Border color.
title	character(1). Title.

Value

Plot.

Note

Updated 2021-02-08.

Examples

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

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

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

acidgenomics/minimalism documentation built on April 1, 2024, 10:34 a.m.