simple_pathview: Print some data onto KEGG pathways.
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

simple_pathview

R Documentation

Print some data onto KEGG pathways.

Description

KEGGREST and pathview provide neat functions for coloring molecular pathways with arbitrary data. Unfortunately they are somewhat evil to use. This attempts to alleviate that.

Usage

simple_pathview(
  gene_input = NULL,
  compound_input = NULL,
  indir = "pathview_in",
  outdir = "pathview",
  pathway = "all",
  species = "lma",
  from_list = NULL,
  to_list = NULL,
  suffix = "_colored",
  id_column = "kegg_ids",
  filenames = "id",
  fc_column = "limma_logfc",
  format = "png",
  verbose = TRUE
)

Arguments

`gene_input`	Some differentially expressed genes.
`compound_input`	Sets of compounds which have changed in the data of interest.
`indir`	Directory into which the unmodified kegg images will be downloaded (or already exist).
`outdir`	Directory which will contain the colored images.
`pathway`	Perform the coloring for a specific pathway?
`species`	Kegg identifier for the species of interest.
`from_list`	Regex to help in renaming KEGG categories/gene names from one format to another.
`to_list`	Regex to help in renaming KEGG categories/gene names from one format to another.
`suffix`	Add a suffix to the completed, colored files.
`id_column`	use this to handle the peculiar ways in which kegg handles IDs.
`filenames`	Name the final files by id or name?
`fc_column`	What is the name of the fold-change column to extract?
`format`	Format of the resulting images, I think only png really works well.
`verbose`	When on, this function is quite chatty.

Value

A list of some information for every KEGG pathway downloaded/examined. This information includes: a. The filename of the final image for each pathway. b. The number of genes which were found in each pathway image. c. The number of genes in the 'up' category d. The number of genes in the 'down' category

Examples

## Not run: 
 thy_el_comp2_path = hpgl_pathview(thy_el_comp2_kegg, species = "spz", indir = "pathview_in",
                                   outdir = "kegg_thy_el_comp2", string_from = "_Spy",
                                   string_to = "_Spy_", filenames = "pathname")

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.