deprecated-heatmap-annotations: DEPRECATED Heatmap annotations helpers

In david-barnett/microViz: Microbiome Data Analysis and Visualization

DEPRECATED Heatmap annotations helpers

Description

Functions to easily define ComplexHeatmap annotations for taxa and/or variables

• tax_anno creates list describing taxa annotation (for cor_heatmap or comp_heatmap)

• var_anno creates list describing variable annotation (for cor_heatmap)

Usage

tax_anno(
  undetected = 0,
  which = NA,
  prev = 1,
  abund = 2,
  size = 30,
  gap = 2,
  rel_sizes = NA,
  args = NULL,
  ...
)

anno_prev(
  data,
  taxa,
  undetected = 0,
  which = "row",
  size = 15,
  bar_width = 0.6,
  gp = grid::gpar(fill = "grey85"),
  ...
)

anno_abund(
  data,
  taxa,
  undetected = 0,
  which = "row",
  size = 15,
  point_size = 0.75,
  box_width = 0.6,
  gp = grid::gpar(fill = "grey85"),
  ...
)

var_anno(
  annos = "var_box",
  funs = "identity",
  names = NA,
  which = "column",
  size = 15 * length(annos),
  gap = 2,
  rel_sizes = NA,
  args = NULL,
  ...
)

old_anno_var_hist(data, vars = NA, which = "column", size = 15, ...)

old_anno_var_box(data, vars = NA, which = "column", size = 15, ...)

Arguments

undetected	value above which taxa are considered present/detected in a sample
which	"row" or "column" annnotation
prev	order in which prevalence annotation shown (number, or NA to not show)
abund	order in which abundance annotation shown (number, or NA to not show)
size	total size (mm) of annotations (width/height depending on which)
gap	gap in mm between annotations
rel_sizes	relative sizes of annotations (NA for equal sizes, or same length as annos)
args	extra args passed to each annotation: give as list of lists (one inner list per arg, named, e.g. list(prev = list(whatever = whatever))
...	further named args to be passed on (to list)
data	phyloseq or ps-extra (or a data.frame or matrix for anno_var_* functions)
taxa	names of taxa to plot
bar_width	relative width of barchart bars
gp	a grid::gpar() object for graphics parameter settings like fill or lwd
point_size	size of outlier points in mm
box_width	relative width of boxplot boxes
annos	name(s) of annotation(s) to show, in order (e.g. 'var_box', 'var_hist')
funs	function(s) to transform matrix of variable values before plotting (length must be 1 or same length as annos)
names	names to use for each annotation in annos
vars	names of variables to plot

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.