We will be offering mothur and R workshops throughout 2019. Learn more.

Pca

From mothur
Jump to: navigation, search

The pca command requires a shared or relabund file.



Default settings

A shared or relabund file must be inputted for pca to be successful.

mothur > pca(shared=genus.pool.shared)

or

mothur > pca(relabund=genus.pool.relabund)

The output to the screen would look something like:

You did not provide a label, I will use the first label in your inputfile.

Processing genus
Rsq 1 axis: 0.777358
Rsq 2 axis: 0.893548
Rsq 3 axis: 0.953764

Options

label

The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.

groups

The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.

metric

The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True

Revisions

  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347