sehm {SEtools}R Documentation

sehm

Description

Heatmap wrapper for SummarizedExperiment-class.

Usage

sehm(se, genes = NULL, do.scale = FALSE,
  assayName = .getDef("assayName"), sortRowsOn = seq_len(ncol(se)),
  cluster_cols = FALSE, cluster_rows = is.null(sortRowsOn),
  toporder = NULL, hmcols = NULL, breaks = .getDef("breaks"),
  gaps_at = .getDef("gaps_at"), gaps_row = NULL,
  anno_rows = .getDef("anno_rows"),
  anno_columns = .getDef("anno_columns"),
  anno_colors = .getDef("anno_colors"), show_rownames = NULL,
  show_colnames = FALSE, ...)

Arguments

se

A SummarizedExperiment-class.

genes

An optional vector of genes (i.e. row names of 'se')

do.scale

Logical; whether to scale rows (default FALSE).

assayName

An optional vector of assayNames to use. The first available will be used, or the first assay if NULL.

sortRowsOn

Sort rows by MDS polar order using the specified columns (default all)

cluster_cols

Whether to cluster columns (default F)

cluster_rows

Whether to cluster rows; default FALSE if 'do.sortRows=TRUE'.

toporder

Optional verctor of categories on which to supra-order when sorting rows, or name of a 'rowData' column to use for this purpose.

hmcols

Colors for the heatmap.

breaks

Breaks for the heatmap colors. Alternatively, if 'breaks==TRUE', a symmetrical scale with capped ends will be used (appropriate when plotting log2 foldchanges)

gaps_at

Columns of 'colData' to use to establish gaps between columns.

gaps_row

Passed to pheatmap; if missing, will be set automatically according to toporder.

anno_rows

Columns of 'rowData' to use for annotation.

anno_columns

Columns of 'colData' to use for annotation.

anno_colors

List of colors to use for annotation.

show_rownames

Whether to show row names (default TRUE if 50 rows or less).

show_colnames

Whether to show column names (default FALSE).

...

Further arguments passed to 'pheatmap'.

Value

A heatmap (see pheatmap).

Examples

data("SE", package="SEtools")
sehm(SE, do.scale=TRUE)


[Package SEtools version 1.0.0 Index]