Heatmap

These functions facilitate heatmap plotting of a specified set of genes. By default, row- and column-wise hierarchical clustering is performed using the Ward method, but this behavior can be overrided by setting cluster_rows or cluster_cols to FALSE. When column clustering is disabled, the columns are sorted by the interesting groups (interestingGroups) specified in the bcbioRNASeq and then the sample names.

plotHeatmap(object, ...)

# S4 method for bcbioRNASeq
plotHeatmap(object, genes = NULL, title = NULL,
  color = inferno(256), legendColor = viridis, quiet = FALSE, ...)

# S4 method for DESeqDataSet
plotHeatmap(object, genes = NULL,
  annotationCol = NULL, title = NULL, color = inferno(256),
  legendColor = viridis, quiet = FALSE, ...)

# S4 method for DESeqTransform
plotHeatmap(object, genes = NULL,
  annotationCol = NULL, title = NULL, color = inferno(256),
  legendColor = viridis, quiet = FALSE, ...)

# S4 method for matrix
plotHeatmap(object, genes = NULL, annotationCol = NULL,
  title = NULL, color = inferno(256), legendColor = viridis,
  quiet = FALSE, ...)

Arguments

object	Object.
...	Passthrough arguments to pheatmap::pheatmap().
genes	Character vector of specific gene identifiers to plot.
title	Optional. Plot title.
color	Colors to use for plot. Defaults to inferno() palette.
legendColor	Colors to use for legend labels. Defaults to viridis() palette.
quiet	If TRUE, suppress any status messages and/or progress bars.
annotationCol	data.frame that specifies the annotations shown on the right side of the heatmap. Each row of this data.frame defines the features of the heatmap columns.

Value

Graphical output only.

See also

pheatmap::pheatmap().

Other Heatmaps: plotCorrelationHeatmap, plotDEGHeatmap

Examples

# Genes as Ensembl identifiers
genes <- counts(bcb)[1:20, ] %>% rownames()
plotHeatmap(bcb, genes = genes)
#> Loading Ensembl annotations from AnnotationHub
#> 2017-10-27
#> EnsDB AH57770: Mus musculus Ensembl 90

# Flip the plot and legend palettes
plotHeatmap(
    bcb,
    genes = genes,
    color = viridis(256),
    legendColor = inferno)
#> Loading Ensembl annotations from AnnotationHub
#> 2017-10-27
#> EnsDB AH57770: Mus musculus Ensembl 90

# Transcriptome heatmap
# NOT RUN {
plotHeatmap(bcb)
# }

# Use default pheatmap color palette
# NOT RUN {
plotHeatmap(
    bcb,
    color = NULL,
    legendColor = NULL)
# }

# DESeqDataSet
# NOT RUN {
plotHeatmap(dds)
# }

# DESeqTransform
# NOT RUN {
plotHeatmap(rld)
# }