create_kegg_map: create_kegg_map

In w-korani/keggseq: KEGG analysis and visualizing of differentially expressed genes

Description

create_kegg_map generates kegg_map with highlighted DEGs for an interested pathway.
the function creates three objects that saved directly to the working dirctory:
"map_number".png: it has the pathway map graph with highlighted differentially expressed genes,
the differentially expressed gene are highlighted by blue color,
the differentially expressed genes that translated in a unque, specific, enzyme for the interested pathway are highlighted by red color.
"map_number"_enzymes.csv": a two column csv file contains the enzyme names and corresponding gene ids included in the interested pathway
"map_number"_de_enzymes.csv: a two column csv file contains the enzyme names and corresponding differentially expressed gene ids included in the interested pathway

Usage

create_kegg_map(species,dataset,deg_list,map_number,correction_file_name)

Arguments

species	A list of abbreviations of the intersested species.
dataset	The output dataset of the calculate_kegg function.
deg_list	A list containing the differentially expressed genes.
map_number	A string of the interested map number.
correction_file_name	An optional filed, a string to file name, and path, of the dataset_alternate_file in case of using corrected_datasets_ids function.

Value

returns pathway graph and open the pathway webpage.

Examples

a <- list_species("arachis")
b <- grep_datasets(c("adu","aip"))
deg_list <- as.matrix(b[b$kegg_pathways=='00061',1])[,1]
c <- calculate_kegg(b,deg_list)
create_kegg_map(c("adu","aip"),c,deg_list,"00480")

w-korani/keggseq documentation built on May 3, 2019, 7:10 p.m.