Generate annotations list — generate_annotations

Intermediate function that takes in formatted lists of features and the annotations they should be viewed through and returns annotation objects usable by ComplexHeatmap::Heatmap.

Usage

generate_annotations_list(
  df,
  left_bar = NULL,
  right_bar = NULL,
  top_bar = NULL,
  bottom_bar = NULL,
  left_hm = NULL,
  right_hm = NULL,
  top_hm = NULL,
  bottom_hm = NULL,
  show_legend = TRUE,
  annotation_colours = NULL
)

Arguments

df: Dataframe containing all the data that is specified in the remaining arguments.
left_bar: Named list of strings, where the strings are features in df that should be used for a barplot annotation on the left of the plot and the names are the names that will be used to caption the plots and their legends.
right_bar: See left_bar.
top_bar: See left_bar.
bottom_bar: See left_bar.
left_hm: Like left_bar, but with a heatmap annotation instead of a barplot annotation.
right_hm: See left_hm.
top_hm: See left_hm.
bottom_hm: See left_hm.
show_legend: Add legends to the annotations.
annotation_colours: Named list of heatmap annotations and their colours.

Value

annotations_list A named list of all the annotations.