sechm: sechm

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

sechm

Description

ComplexHeatmap wrapper for SummarizedExperiment-class.

Usage

sechm(
  se,
  features,
  do.scale = FALSE,
  assayName = NULL,
  name = NULL,
  sortRowsOn = NULL,
  cluster_cols = FALSE,
  cluster_rows = NULL,
  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 Nov. 15, 2024, 5:08 a.m.