Metabolism PCA.

Source: R/GET-get_pca.R, R/GET-get_subset_pca.R

Identifies the most important KO pathways or protein domains in the whole database. And print back a profile of the protein domains that have higher contributions.

Identifies the most important KO pathways or protein domains in the whole database. And print back a profile of the protein domains that have higher contributions.

get_subset_pca(tibble_rbims, cos2_val=NULL, 
analysis=c("KEGG", "Pfam", "INTERPRO"))

get_subset_pca(tibble_rbims, cos2_val=NULL, 
analysis=c("KEGG", "Pfam", "INTERPRO"))

Arguments

tibble_rbims

a tibble object, created with the read_interpro, mapping_ko or get_subset_* functions.

cos2_val

a numeric vector from 0 to 1 indicating the proportion of contribution used as cut off. Default is 0.98. See get_pca.

analysis

a character, indicating from which input do you want to get the abundance profile. Valid options are "KEGG", "Pfam" or "INTERPRO".

Details

This function is part of a package used for the analysis of bins metabolism.

This function is part of a package used for the analysis of bins metabolism.

Examples

#get_subset_pca(ko_bin_mapp, analysis="KEGG")
#get_subset_pca(ko_bin_mapp, analysis="KEGG")