calculate_gap: Calculate the gaps based on distance

In gapmap: Functions for Drawing Gapped Cluster Heatmap with ggplot2

Description

This function takes a dendrogram class object and other attributes to calcuate the size of gaps between leaves. The gap is stored in a leaf to its left. The function is called recursively.

Usage

calculate_gap(d, sum, gap_total, mode = c("quantitative", "threshold"),
  mapping = c("exponential", "linear"), scale = 0.2, max_height = 0,
  threshold = 2, gap_size = 0, verbose = FALSE, ...)

Arguments

d	dendrogram class object
sum	the sum of distance
gap_total	the total width allocated for gaps
mode	gap mode, either "threshold" or "quantitative"
mapping	in case of quantitative mode, either "linear" or "exponential" mapping
scale	the sclae log base for the exponential mapping
max_height	the highest distance value, which is the value of the first dendrogram branch
threshold	the threshold value for threshold mode
gap_size	the size of gap for threshold mode
verbose	logical for whether in verbose mode or not
...	ignored

Value

the annotated dendrogram class object

gapmap documentation built on May 29, 2017, 7 p.m.

Re-evaluate the position of leaves

gapmap index

Count the number of gaps based on a threshold