gap_data {gapmap}

Generate a gapdata class object from a dendrogram object

Description

This function takes a dendrogram class object as an input, and generate a gapdata class object as an output. By parsing the dendrogram object based on parameters for gaps, gaps between leaves in a dendrogram are introduced, and the coordinates of the leaves are adjusted. The gaps can be based on the a height (or distance) threshold to to introduce the gaps of the same width, or quantitative mapping of distance values mapped linearly or exponentially.

Usage

gap_data(
  d,
  mode = c("quantitative", "threshold"),
  mapping = c("exponential", "linear"),
  ratio = 0.2,
  scale = 0.5,
  threshold = 0,
  verbose = FALSE,
  ...
)

Arguments

d

dendrogram class object

mode

gap mode, either "threshold" or "quantitative"

mapping

in case of quantitative mode, either "linear" or "exponential" mapping

ratio

the percentage of width allocated for the sum of gaps.

scale

the sclae log base for the exponential mapping

threshold

the height at which the dendrogram is cult to infer clusters

verbose

logical for whether in verbose mode or not

...

ignored

Value

a list of data frames that contain coordinates for drawing a gapped dendrogram