plotHeatmap: Plot Heatmap

Description Usage Arguments Value See Also Examples

Description

Construct a simple heatmap. By default, row- and column-wise hierarchical clustering is performed using the Ward method, but this behavior can be overrided by setting clusterRows or clusterCols to FALSE.

Usage

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plotHeatmap(object, ...)

## S4 method for signature 'matrix'
plotHeatmap(object, scale = c("row", "column", "none"),
  annotationCol = NULL, clusterRows = TRUE, clusterCols = TRUE,
  showRownames = FALSE, showColnames = TRUE, treeheightRow = 0L,
  treeheightCol = 50L, color = viridis, legendColor = NULL,
  borderColor = NULL, title = NULL, ...)

## S4 method for signature 'dgCMatrix'
plotHeatmap(object, scale = c("row", "column", "none"),
  annotationCol = NULL, clusterRows = TRUE, clusterCols = TRUE,
  showRownames = FALSE, showColnames = TRUE, treeheightRow = 0L,
  treeheightCol = 50L, color = viridis, legendColor = NULL,
  borderColor = NULL, title = NULL, ...)

## S4 method for signature 'dgTMatrix'
plotHeatmap(object, scale = c("row", "column", "none"),
  annotationCol = NULL, clusterRows = TRUE, clusterCols = TRUE,
  showRownames = FALSE, showColnames = TRUE, treeheightRow = 0L,
  treeheightCol = 50L, color = viridis, legendColor = NULL,
  borderColor = NULL, title = NULL, ...)

## S4 method for signature 'SummarizedExperiment'
plotHeatmap(object, interestingGroups, ...)

Arguments

object

Object.

...

Passthrough arguments to pheatmap::pheatmap(). The names of the arguments should be formatted in camel case, not snake case.

scale

character indicating whether the values should be centered and scaled in either the row or column direction ("row", "column"), or remain unscaled ("none").

annotationCol

Optional. data.frame that defines annotation mappings for the columns.

clusterRows, clusterCols

logical determining if rows or columns should be arranged with hierarchical clustering. Alternatively, can define an hclust object.

showRownames, showColnames

Show row or column names.

treeheightRow, treeheightCol

Size of the row and column dendrograms. Use "0" to disable.

color

Colors to use for plot. Defaults to the viridis::viridis() palette.

legendColor

Colors to use for legend labels.

borderColor

Optional. Border color. Disabled by default for improved aesthetics.

title

Optional. Plot title.

interestingGroups

character. Groups of interest.

Value

Show heatmap and invisibly return a list of the components.

See Also

pheatmap::pheatmap().

Other Plot Functions: plotCorrelationHeatmap, plotQuantileHeatmap

Examples

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# SummarizedExperiment ====
plotHeatmap(rse_dds)

# Disable column clustering
plotHeatmap(rse_dds, clusterCols = FALSE)

hbc/bcbioBase documentation built on July 10, 2018, 3:50 p.m.