mark.pathway.by.objects: Client-side interface to obtain an url for a KEGG pathway...

View source: R/KEGGREST.R

mark.pathway.by.objectsR Documentation

Client-side interface to obtain an url for a KEGG pathway diagram with a given set of genes marked

Description

Given a KEGG pathway id and a set of KEGG gene ids, the functions return the URL of a KEGG pathway diagram with the elements corresponding to the genes marked by red or specified color

Usage

mark.pathway.by.objects(pathway.id, object.id.list)
color.pathway.by.objects(pathway.id, object.id.list,
                                     fg.color.list, bg.color.list)

Arguments

pathway.id

pathway.id a character string for a KEGG pathway id. KEGG pathway ids consist of the string path followed by a colon, a three-letter code for the organism of concern, and then a number (e. g. "path:eco00020"). The three-letter organism code consists of the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern

object.id.list

object.id.list a vector of character strings for KEGG gene ids. KEGG gene ids normally consist of three letters followed by a column and then several numeric numbers. The three letters are from the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern (e. g. hsa:111 for Homo Sapiens)

fg.color.list

fg.color.list a vector of two character strings to indicate the color for the text and border, respectively, of the objects in a pathway diagram. The strings can either be a color code linke \#ff0000 or letter link yellow

bg.color.list

bg.color.list a vector of character strings of the same length of object.id.list to indicate the background color of the objects in a pathway diagram. The strings can either be a color code like \#ff0000 or letter like yellow

Details

This function only returns the URL of the KEGG pathway diagram. Use the function browseURL to view the diagram.

These functions are not part of the KEGG REST API; they are provided because they existed in KEGGSOAP and an alternative implementation was possible.

Value

This function returns a character string for the url

Author(s)

Jianhua Zhang

References

https://www.kegg.jp/kegg/docs/keggapi.html

See Also

browseURL

Examples

 url <- mark.pathway.by.objects(
    "path:eco00260", c("eco:b0002", "eco:c00263")
)
if(interactive()){
    browseURL(url)
}
url <- color.pathway.by.objects(
    "path:eco00260", c("eco:b0002", "eco:c00263"),
    c("#ff0000", "#00ff00"),
    c("#ffff00", "yellow")
)

Bioconductor/KEGGREST documentation built on July 14, 2022, 9:40 p.m.