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more modest output in examples

Martin Morgan authored on 26/06/2018 20:52:11
Showing1 changed files
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@@ -49,20 +49,22 @@ color.pathway.by.objects(pathway.id, object.id.list,
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 \value{
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   This function returns a character string for the url
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 }
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-\references{\url{http://www.kegg.jp/kegg/docs/keggapi.html}}
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+\references{\url{https://www.kegg.jp/kegg/docs/keggapi.html}}
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 \author{Jianhua Zhang}
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 \seealso{\code{\link{browseURL}}}
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 \examples{
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-        url <- mark.pathway.by.objects("path:eco00260",
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-                       c("eco:b0002", "eco:c00263"))
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-        if(interactive()){
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-            browseURL(url)
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-        }
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-       url <- color.pathway.by.objects("path:eco00260",
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-                       c("eco:b0002", "eco:c00263"),
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-                       c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))
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- 
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+ url <- mark.pathway.by.objects(
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+    "path:eco00260", c("eco:b0002", "eco:c00263")
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+)
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+if(interactive()){
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+    browseURL(url)
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+}
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+url <- color.pathway.by.objects(
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+    "path:eco00260", c("eco:b0002", "eco:c00263"),
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+    c("#ff0000", "#00ff00"),
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+    c("#ffff00", "yellow")
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+)
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 }
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 \keyword{ datasets }
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Browse code

progress on vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72345 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 08/01/2013 00:19:14
Showing1 changed files
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@@ -40,7 +40,11 @@ color.pathway.by.objects(pathway.id, object.id.list,
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 }
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 \details{
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   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
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+  the function \code{\link{browseURL}} to view the diagram.
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+
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+  These functions are not part of the KEGG REST API; they are provided
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+  because they existed in \code{KEGGSOAP} and an alternative implementation
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+  was possible.
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 }
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 \value{
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   This function returns a character string for the url
Browse code

passes check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72162 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 24/12/2012 02:23:33
Showing1 changed files
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@@ -45,7 +45,7 @@ color.pathway.by.objects(pathway.id, object.id.list,
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 \value{
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   This function returns a character string for the url
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 }
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-\references{\url{http://www.genome.jp/kegg/soap/doc/keggapi_manual.html}}
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+\references{\url{http://www.kegg.jp/kegg/docs/keggapi.html}}
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 \author{Jianhua Zhang}
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 \seealso{\code{\link{browseURL}}}
Browse code

initial checkin, only one function works (get.genes.by.pathway())

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72144 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 22/12/2012 02:17:15
Showing1 changed files
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new file mode 100644
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@@ -0,0 +1,64 @@
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+\name{mark.pathway.by.objects}
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+\alias{mark.pathway.by.objects}
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+\alias{color.pathway.by.objects}
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+
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+\title{Client-side interface to obtain an url for a KEGG pathway diagram
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+with a given set of genes marked}
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+\description{
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+  Given a KEGG pathway id and a set of KEGG gene ids, the functions
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+  return the URL of a KEGG pathway diagram with the elements
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+  corresponding to the genes marked by red or specified color
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+}
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+\usage{
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+mark.pathway.by.objects(pathway.id, object.id.list)
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+color.pathway.by.objects(pathway.id, object.id.list,
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+                                     fg.color.list, bg.color.list)
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+}
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+
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+\arguments{
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+  \item{pathway.id}{\code{pathway.id} a character string for a KEGG
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+    pathway id. KEGG pathway ids consist of the string path followed by
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+    a colon, a three-letter code for the organism of concern, and then
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+    a number (e. g. "path:eco00020"). The three-letter organism code
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+    consists of the first letter of the genus name and the first two
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+    letters of the species name of the scientific name of the organism
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+    of concern}
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+  \item{object.id.list}{\code{object.id.list} a vector of character
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+    strings for KEGG gene ids. KEGG gene ids normally consist of
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+    three letters followed by a column and then several numeric
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+    numbers. The three letters are from the first letter of the genus
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+    name and the first two letters of the species name of the scientific
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+    name of the organism of concern (e. g. hsa:111 for Homo Sapiens)}
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+  \item{fg.color.list}{\code{fg.color.list} a vector of two character
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+    strings to indicate the color for the text and border, respectively,
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+    of the objects in a pathway diagram. The strings can either be a
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+    color code linke \#ff0000 or letter link yellow}
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+  \item{bg.color.list}{\code{bg.color.list} a vector of character
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+    strings of the same length of \code{object.id.list} to indicate the
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+    background color of the objects in a pathway diagram. The strings
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+    can either be a color code like \#ff0000 or letter like yellow}
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+}
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+\details{
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+  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
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+}
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+\value{
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+  This function returns a character string for the url
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+}
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+\references{\url{http://www.genome.jp/kegg/soap/doc/keggapi_manual.html}}
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+\author{Jianhua Zhang}
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+
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+\seealso{\code{\link{browseURL}}}
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+\examples{
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+        url <- mark.pathway.by.objects("path:eco00260",
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+                       c("eco:b0002", "eco:c00263"))
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+        if(interactive()){
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+            browseURL(url)
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+        }
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+       url <- color.pathway.by.objects("path:eco00260",
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+                       c("eco:b0002", "eco:c00263"),
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+                       c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))
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+ 
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+}
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+\keyword{ datasets }
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+