save.eigenplots.html: Generate HTML file for EigenFit plots

In kridsadakorn/ipcaps.bioc: Iterative Pruning to Capture Population Structure

Description

Generate HTML file called 'tree_scree.html' from the result of ipcaps. This function is a part of workflow in save.plots. The clustering result is shown as a tree rendering by the online Google Organizational Chart library. Note that the Internet is required to view the HTML file.

Usage

save.eigenplots.html(output.dir)

Arguments

output.dir

A result directory as the $output object returned from the ipcaps function.

Details

After running, this function generates the file called 'tree_scree.html' in the same result directory. All plots are generated and saved as image files in the sub-directory 'images'.

Value

NULL

See Also

save.html, save.plots, save.plots.cluster.html, and save.plots.label.html

Examples

# Importantly, bed file, bim file, and fam file are required
# Use the example files embedded in the package

BED.file <- system.file('extdata',
                        'ipcaps_example.bed',
                        package = 'IPCAPS.BIOC')

LABEL.file <- system.file('extdata',
                          'ipcaps_example_individuals.txt.gz',
                          package = 'IPCAPS.BIOC')

my.cluster <- ipcaps(bed = BED.file,
                     label.file = LABEL.file,
                     lab.col = 2,
                     out = tempdir(),
                     max.thread = 1,
                     seed = 1234)

#Here, to generate HTML file
save.eigenplots.html(my.cluster$output.dir)

kridsadakorn/ipcaps.bioc documentation built on Jan. 22, 2020, 11:18 p.m.