crossHm {SEtools}R Documentation

crossHm

Description

Plot a multi-panel heatmap from a list of SummarizedExperiment-class

Usage

crossHm(ses, genes, do.scale = TRUE, uniqueColorScale = FALSE,
  assayName = .getDef("assayName"), do.sortRows = TRUE,
  only.common = TRUE, anno_columns = .getDef("anno_columns"),
  spreadAnnotation = FALSE, hmcols = NULL, cluster_columns = FALSE,
  cluster_rows = !do.sortRows, show_rownames = ifelse(length(genes) <
  80, "once", FALSE), show_colnames = FALSE,
  anno_colors = .getDef("anno_colors"), ...)

Arguments

ses

A (named) list of SummarizedExperiment-class.

genes

A vector of genes/row.names to plot.

do.scale

Logical; whether to scale rows in each SE (default TRUE).

uniqueColorScale

Logical; whether to force the same colorscale for each heatmap (default FALSE; applicable only when what!='asis').

assayName

The name of the assay to use; if multiple names are given, the first available will be used. Defaults to "logcpm", "lognorm".

do.sortRows

Logical; whether to sort rows according to MDS (default TRUE).

only.common

Logical; whether to plot only rows common to all SEs (default TRUE).

anno_columns

A vector of colData columns to use (if available) for annotation, default "Condition" and "TimePoint".

spreadAnnotation

Logical; whether to spread annotation to all SEs (not yet supported)

hmcols

An optional color palette, such as produced by the 'colorRampPalette' function.

cluster_columns

Logical; whether to cluster columns (default FALSE).

cluster_rows

Logical; whether to cluster rows (default TRUE if 'do.sortRows=FALSE', FALSE otherwise).

show_rownames

Logical; whether to show row names (default TRUE if 'length(genes)<80', FALSE otherwise).

show_colnames

Logical; whether to show column names (default FALSE)

anno_colors

A vector of color for annotations.

...

Any other parameter passed to each call of Heatmap.

Value

A Heatmap-class object.

Examples

data("SE", package="SEtools")
crossHm(list(se1=SE[,1:10], se2=SE[,11:20]), head(row.names(SE)))


[Package SEtools version 1.0.0 Index]