crossHm: crossHm

In plger/sechm: sechm: Complex Heatmaps from a SummarizedExperiment

crossHm

Description

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

Usage

crossHm(
  ses,
  features,
  do.scale = TRUE,
  uniqueScale = FALSE,
  assayName = .getDef("assayName"),
  sortBy = seq_along(ses),
  only.common = TRUE,
  cluster_cols = FALSE,
  cluster_rows = is.null(sortBy),
  toporder = NULL,
  hmcols = NULL,
  breaks = .getDef("breaks"),
  gaps_at = .getDef("gaps_at"),
  gaps_row = NULL,
  name = NULL,
  top_annotation = .getDef("anno_columns"),
  left_annotation = .getDef("anno_rows"),
  anno_colors = list(),
  show_rownames = NULL,
  merge_legends = FALSE,
  show_colnames = FALSE,
  rel.width = NULL,
  ...
)

Arguments

ses	A (named) list of SummarizedExperiment-class objects, with some matching row.names between them.
features	A vector of features (i.e. row.names) to plot.
do.scale	Logical; whether to scale rows in each SE (default TRUE).
uniqueScale	Logical; whether to force the same colorscale for each heatmap.
assayName	The name of the assay to use; if multiple names are given, the first available will be used. Defaults to "logcpm", "lognorm".
sortBy	Names or indexes of 'ses' to use for sorting rows (default all)
only.common	Logical; whether to plot only rows common to all SEs (default TRUE).
cluster_cols	Logical; whether to cluster columns (default FALSE).
cluster_rows	Logical; whether to cluster rows (default TRUE if 'do.sortRows=FALSE', FALSE otherwise).
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, symmetrical breaks can be generated automatically by setting 'breaks' to a numerical value between 0 and 1. The value is passed as the 'split.prop' argument to the getBreaks function, and indicates the proportion of the points to map to a linear scale, while the more extreme values will be plotted on a quantile scale. 'breaks=FALSE' will disable symmetrical scale and quantile capping, while retaining automatic breaks. 'breaks=1' will produce a symmetrical scale without quantile capping.
gaps_at	Columns of 'colData' to use to establish gaps between columns.
gaps_row	A named vector according to which rows will be split.
name	The title of the heatmap key.
top_annotation	Columns of 'colData' to use for top annotation.
left_annotation	Columns of 'rowData' to use for left annotation.
anno_colors	List of colors to use for annotation.
show_rownames	Whether to show row names (default TRUE if 50 rows or less).
merge_legends	Logical; passed to draw-HeatmapList-method
show_colnames	Whether to show column names (default FALSE).
rel.width	Relative width of the heatmaps
...	Any other parameter passed to each call of Heatmap.

Value

A Heatmap list.

Examples

data("Chen2017", package="sechm")
se1 <- Chen2017[,1:6]
se2 <- Chen2017[,7:15]
se3 <- crossHm(list(se1=se1, se2=se2), row.names(se1)[1:10] )

plger/sechm documentation built on Nov. 15, 2024, 5:08 a.m.