heatmap_annotated: Annotated heatmap

In vittoriofortino84/COPS: Clustering algorithms for Omics-driven Patient Stratification

Annotated heatmap

Description

Generate a heatmap with annotations.

Usage

heatmap_annotated(
  dat,
  variable_list = list(),
  feature_names = NULL,
  center = TRUE,
  scale = FALSE,
  show_column_names = FALSE,
  show_row_names = TRUE,
  show_column_dend = FALSE,
  show_row_dend = FALSE,
  row_names_side = "left",
  legend_names = NULL,
  color_breaks = NULL,
  heatmap_color_function = circlize::colorRamp2(color_breaks, c("blue", "white", "red")),
  ...
)

Arguments

dat	feature matrix or list of matrices, samples on columns
variable_list	list of column annotation variables
feature_names	optional character vector matching to a subset of dat rownames
center	whether to apply row-wise center, passed to scale
scale	whether to apply row-wise scaling, passed to scale
show_column_names	whether to include colnames (sample names)
show_row_names	whether to include rownames (gene names)
show_column_dend	whether to include column dendrogram
show_row_dend	whether to include row dendrogram
row_names_side	where row names should be located
legend_names	names to use for dat color legends
color_breaks	manual color breaks in form c(min, middle, max)
heatmap_color_function	passed to Heatmap as col
...	other arguments passed to Heatmap

Value

'HeatmapList-class'

vittoriofortino84/COPS documentation built on Jan. 28, 2025, 3:16 p.m.