mark.pathway.by.objects {KEGGSOAP} | R Documentation |
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
mark.pathway.by.objects(pathway.id, object.id.list) color.pathway.by.objects(pathway.id, object.id.list, fg.color.list, bg.color.list)
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 |
This function only returns the URL of the KEGG pathway diagram. Use
the function browseURL
to view the diagram
This function returns a character string for the url
Jianhua Zhang
http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
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"))