SE-heatmap {SEtools}R Documentation

Heatmap wrappers for SummarizedExperiment-class.

Description

These functions have been moved and will be deprecated from this package; please use the [sechm](https://bioconductor.org/packages/release/bioc/html/sechm.html) package instead.

Usage

sechm(
  se,
  genes,
  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"),
  name = NULL,
  anno_colors = list(),
  show_rownames = NULL,
  show_colnames = FALSE,
  isMult = FALSE,
  show_heatmap_legend = !isMult,
  show_annotation_legend = TRUE,
  annorow_title_side = ifelse(show_colnames, "bottom", "top"),
  mark = NULL,
  right_annotation = NULL,
  includeMissing = FALSE,
  sort.method = "MDS_angle",
  ...
)

sehm(
  se,
  genes,
  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 = .getAnnoCols(se),
  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, 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

Passed to the heatmap function; 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.

name

The name of the heatmap, eventually appearing as title of the color scale.

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).

isMult

Logical; used to silence labels when plotting mulitple heatmaps

show_heatmap_legend

Logical; whether to show heatmap legend

show_annotation_legend

Logical; whether to show the annotation legend.

mark

An optional vector of gene names to highlight.

right_annotation

Passed to 'ComplexHeatmap::Heatmap'

includeMissing

Logical; whether to include missing genes (default FALSE)

sort.method

Method to use for row sorting (see sortRows)

...

Further arguments passed to 'pheatmap' ('sehm') or 'Heatmap' ('sechm').

annorows_title_side

Side (top or bottom) of row annotation names

Value

A a Heatmap-class.

Examples

data("SE", package="SEtools")
sehm(SE, row.names(SE)[1:10], do.scale=TRUE)


[Package SEtools version 1.6.0 Index]