man/mark.pathway.by.objects.Rd
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 \name{mark.pathway.by.objects}
 \alias{mark.pathway.by.objects}
 \alias{color.pathway.by.objects}
 
 \title{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{
   \item{pathway.id}{\code{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}
   \item{object.id.list}{\code{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)}
   \item{fg.color.list}{\code{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}
   \item{bg.color.list}{\code{bg.color.list} a vector of character
     strings of the same length of \code{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
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   the function \code{\link{browseURL}} to view the diagram.
 
   These functions are not part of the KEGG REST API; they are provided
   because they existed in \code{KEGGSOAP} and an alternative implementation
   was possible.
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 }
 \value{
   This function returns a character string for the url
 }
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 \references{\url{https://www.kegg.jp/kegg/docs/keggapi.html}}
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 \author{Jianhua Zhang}
 
 \seealso{\code{\link{browseURL}}}
 \examples{
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  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")
 )
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 }
 \keyword{ datasets }