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.