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Generates pdf report with colored pathways and plots

Source: R/fast_psf_functions.R
generate_psf_report.Rd

Generates pdf report with colored pathways and plots

Usage

generate_psf_report(
  psf_list,
  folder_name,
  plot_type = "kegg",
  log_norm = TRUE,
  y_adj_text = 0,
  y_adj_sink = 0,
  use_old_images = F
)

Arguments

psf_list

Output from run_psf function

folder_name

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

plot_type

Pathway visualization type. Possible values are c("kegg", "visnet"). Default value is "kegg".

log_norm

log transform PSF values before color mapping. Default value is TRUE.

y_adj_text

Numeric value to adjust Y position of node labels. Depending on R version this value should be adjusted to have accurate text alignment. Default value is 0.

y_adj_sink

Numeric value to adjust Y position of sink node sign labels. Depending on R version this value should be adjusted to have accurate alignment. Default value is 0.

use_old_images

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