save.plots: Workflow to generate HTML files for all kinds of plots

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

Description

Generate HTML files and all image files (plots) from the result of ipcaps. 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 files.

Usage

save.plots(output.dir)

Arguments

output.dir

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

Details

After running, this function generates all plots and saves as image files in the sub-directory 'images'. It calls save.plots.cluster.html, save.eigenplots.html, and save.plots.label.html to generate all HTML files.

Value

NULL

See Also

save.html, save.plots.cluster.html, save.eigenplots.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 all plots and HTML files
save.plots.label.html(my.cluster$output.dir)

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