save.plots: Workflow to generate HTML files for all kinds of plots
In IPCAPS: Iterative Pruning to Capture Population Structure

Description Usage Arguments Details Value See Also Examples

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.

1	save.plots(output.dir)

output.dir

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

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.

NULL

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

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

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

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