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

In kridsadakorn/ipcaps2: Iterative Pruning to Capture Population Structure version 2

Workflow to generate HTML files for all kinds of plots

Description

Generate HTML files and all image files (plots) from the result of ipcaps2. 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 ipcaps2 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="IPCAPS2")
LABEL.file <- system.file("extdata","ipcaps_example_individuals.txt.gz",package="IPCAPS2")

my.cluster <- ipcaps2(bed=BED.file,
                      label.file=LABEL.file,
                      lab.col=2,
                      out=tempdir(),
                      silence=TRUE,
                      no.rep=1)

#Here, to generate all plots and HTML files
save.plots.label.html(my.cluster$output.dir)

kridsadakorn/ipcaps2 documentation built on June 11, 2022, 8:35 p.m.