sechm: sechm

View source: R/sechm.R

sechmR Documentation

sechm

Description

ComplexHeatmap wrapper for SummarizedExperiment-class.

Usage

sechm(
  se,
  features,
  do.scale = FALSE,
  assayName = NULL,
  name = NULL,
  sortRowsOn = seq_len(ncol(se)),
  cluster_cols = FALSE,
  cluster_rows = is.null(sortRowsOn),
  toporder = NULL,
  hmcols = NULL,
  breaks = .getDef("breaks"),
  gaps_at = NULL,
  gaps_row = NULL,
  left_annotation = NULL,
  right_annotation = NULL,
  top_annotation = NULL,
  bottom_annotation = NULL,
  anno_colors = list(),
  show_rownames = NULL,
  show_colnames = FALSE,
  isMult = FALSE,
  show_heatmap_legend = !isMult,
  show_annotation_legend = TRUE,
  mark = NULL,
  na_col = "white",
  annorow_title_side = ifelse(show_colnames, "bottom", "top"),
  annocol_title_side = "right",
  includeMissing = FALSE,
  sort.method = "MDS_angle",
  ...
)

Arguments

se

A SummarizedExperiment-class.

features

A vector of features (i.e. row names of 'se'). Alternatively, can be a list of feature sets, in which case these will be plotted as different row chunks.

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.

name

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

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 vector 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.

left_annotation

Columns of 'rowData' to use for left annotation. Alternatively, an 'HeatmapAnnotation' object.

right_annotation

Columns of 'rowData' to use for left annotation. Alternatively, an 'HeatmapAnnotation' object.

top_annotation

Columns of 'colData' to use for top annotation. Alternatively, an 'HeatmapAnnotation' object. To disable (overriding defaults), use 'top_annotation=character()'.

bottom_annotation

Columns of 'colData' to use for bottom annotation. Alternatively, an 'HeatmapAnnotation' object.

anno_colors

List of colors to use for annotation.

show_rownames

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

show_colnames

Whether to show column names (default FALSE).

isMult

Logical; used to silence labels when plotting multiple 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.

na_col

Color of NA values

annorow_title_side

Side (top or bottom) of row annotation names

annocol_title_side

Side (left or right) of column annotation names

includeMissing

Logical; whether to include missing features (default FALSE)

sort.method

Row sorting method (see sortRows)

...

Further arguments passed to 'Heatmap'

Value

A a Heatmap-class.

Examples

data("Chen2017", package="sechm")
sechm(Chen2017, row.names(Chen2017)[1:10], do.scale=TRUE)


plger/sechm documentation built on June 16, 2024, 7:53 a.m.