plotOverlaps: plot cluster-cluster or segment-segment overlaps

Description Usage Arguments

View source: R/clusterTools.R

Description

Plots the significance distribution of cluster-cluster or segment-segment overlap statistics provided by clusterCluster or segmentJaccard, where the a white-black gradient is calculated from -log(p), and the text shows the overlap statistics, i.e., the number of overlapping features for clusterCluster, or the Jaccard index for segmentJaccard. Note that two distinct p-value cutoffs can be visualyized: p-values <=p.min are shown in black, and p-values p.txt are shown in white instead of black text (thus becoming visible on the black of significant overlaps).

Usage

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plotOverlaps(x, p.min = 0.01, p.txt = p.min * 5, n = 100, col,
  short = TRUE, scale = 1, round, axis = 1:2, ...)

Arguments

x

a ‘clusterOverlaps’ object returned by clusterCluster

p.min

significance cutoff, p-values equal or smaller to this cutoff will appear black; TODO: plot legend

p.txt

p-value cutoff for showing overlap numbers as white instead of black text

n

number of color shades between p=1 (white) and p >= p.min (black)

col

color ramp, default are grey values, length of this vector overrules parameter n

short

logical, indicating whether to cut higher overlap numbers; currently: division by 1000 and replacement by k

scale

factor to divide overlap numbers with, useful for low numbers in Jaccard index

round

number of digits to round overlap numbers to (useful for Jaccard index)

axis

integer vector, sets whether x-axis (1,3) and/or y-axis (2,4) are drawn; the column and row names of dat will be used as tick labels

...

arguments to image_matrix


raim/segmenTools documentation built on Nov. 9, 2018, 5:38 p.m.