In bennop/clusterLUTs: Color lookup ables for use with hierarchical clustering

knitr::opts_chunk$set(echo = TRUE,
                      collapse = TRUE,
                      comment = "#>"
)

library(clusterLUTs)

Load Atlas File

Atlas file is located in current working directory so simply read it

atlas <- read.tree(system.file('extdata/sbm_1_145_0_atlas.mat',
                               package = 'clusterLUTs'))

By default a column for individual areas is added if that is not present in the input file.

Create LUT files

The LUTs are derived directly from the atlas file with a single call to treeluts:

tl <- treeluts(atlas, outdir = '.', basename = 'oct_')

This command also creates the *lut files in the current directory.

Visualization

To visualize the LUTs create the tree and plot it

tr <- tree.ranges(atlas)
tree.ranges.plot(tr, show.tree = TRUE, lwd = 10, lend = 1)

Note: The order of colors does NOT correspond to the cluster indices in the atlas file.

bennop/clusterLUTs documentation built on Nov. 21, 2020, 9:07 a.m.