Correlation heatmap

plotCorrelationHeatmap(object, ...)

# S4 method for 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.color",
  default = acidplots::synesthesia), legendColor = getOption(x =
  "acid.heatmap.color", default = acidplots::synesthesia),
  borderColor = NULL, title = TRUE, ...)

# S4 method for SingleCellExperiment
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.color",
  default = acidplots::synesthesia), legendColor = getOption(x =
  "acid.heatmap.color", default = acidplots::synesthesia),
  borderColor = NULL, title = TRUE, ...)

Arguments

object

Object.

assay

vector(1). Name or index of count matrix slotted in assays(). When passing in a string, the name must be defined in assayNames().

interestingGroups

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

method

character(1). Correlation coefficient (or covariance) method to be computed. Defaults to "pearson" but "spearman" or "kendall" can also be used. Refer to the stats::cor() documentation for details.

clusteringMethod

character(1). Clustering method. Accepts the same values as hclust().

showRownames

logical(1). Show row or column names.

showColnames

logical(1). Show row or column names.

treeheightRow

integer(1). Size of the row and column dendrograms. Use 0 to disable.

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:

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. Disabled by default for improved aesthetics.

title

character(1). Plot title.

...

Additional arguments.

Value

pheatmap.

Examples

data(rse, sce, package = "acidtest") ## SummarizedExperiment ==== plotCorrelationHeatmap(rse)
#> Calculating correlation matrix using pearson method.
## SingleCellExperiment ==== plotCorrelationHeatmap(sce)
#> Aggregating counts using mean().
#> Calculating correlation matrix using pearson method.