Calculates psf for given kegg pathway based on expression matrix and generates pdf report with colored pathways and plots

Calculates psf for given kegg pathway based on expression matrix and generates pdf report with colored pathways and plots

Usage

calc_psf_and_generate_report_from_collection(
  kegg_collection,
  exp_matrix,
  folder_name,
  calculate_significance = FALSE,
  use_old_images = F,
  coldata = NULL,
  adj = c(0.48, 1)
)

Arguments

kegg_collection

list of kegg pathways

exp_matrix

expression fold change matrix with gene entrez id rownames

folder_name

name of the folder where pdf report(s) will be generated

calculate_significance

logical, if true then psf function will also calculate significance for the PSF values by shuffling all the network nodes and checking if the resulted PSF values were calculated by chance. When set to true volcano plot will be generetaed in pdf report.

use_old_images

use olde kegg images(for use with curated pathway collection)

coldata

table of sample information where first column of the table corresponds to colnames of exp_matrix and the second column is a group information.

adj

two values in between 0 and 1 which specify the x and y adjustment of the node labels, with 0 for left/bottom, 1 for right/top, and 0.5 for centered. Default value is c(0.48, 1). On most devices values outside 0 and 1 will also work.