@@ -49,20 +49,22 @@ color.pathway.by.objects(pathway.id, object.id.list,

 \value{

   This function returns a character string for the url

 }

-\references{\url{http://www.kegg.jp/kegg/docs/keggapi.html}}

+\references{\url{https://www.kegg.jp/kegg/docs/keggapi.html}}

 \author{Jianhua Zhang}

 \seealso{\code{\link{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"))

- 

+ 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 }

@@ -40,7 +40,11 @@ color.pathway.by.objects(pathway.id, object.id.list,

 }

 \details{

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

-  the function \code{\link{browseURL}} to view the diagram

+  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

@@ -45,7 +45,7 @@ color.pathway.by.objects(pathway.id, object.id.list,

 \value{

   This function returns a character string for the url

 }

-\references{\url{http://www.genome.jp/kegg/soap/doc/keggapi_manual.html}}

+\references{\url{http://www.kegg.jp/kegg/docs/keggapi.html}}

 \author{Jianhua Zhang}

 \seealso{\code{\link{browseURL}}}

new file mode 100644

@@ -0,0 +1,64 @@

+\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

+  the function \code{\link{browseURL}} to view the diagram

+}

+\value{

+  This function returns a character string for the url

+}

+\references{\url{http://www.genome.jp/kegg/soap/doc/keggapi_manual.html}}

+\author{Jianhua Zhang}

+

+\seealso{\code{\link{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"))

+ 

+}

+\keyword{ datasets }

+