\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
\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
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.
}
\value{
This function returns a character string for the url
}
\references{\url{https://www.kegg.jp/kegg/docs/keggapi.html}}
\author{Jianhua Zhang}

\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")
)
}
\keyword{ datasets }