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

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

Generate HTML file for EigenFit plots

Description

Generate HTML file called 'tree_scree.html' from the result of ipcaps2. 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 ipcaps2 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="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 HTML file
save.eigenplots.html(my.cluster$output.dir)

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