DEPRECATED Heatmap annotations helpers

Source: R/heatmap_annotations-deprecated.R

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)

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