#### more modest output in examples

Martin Morgan authored on 26/06/2018 20:52:11
Showing1 changed files
 ... ... @@ -49,20 +49,22 @@ color.pathway.by.objects(pathway.id, object.id.list, 49 49  \value{ 50 50  This function returns a character string for the url 51 51  } 52 -\references{\url{http://www.kegg.jp/kegg/docs/keggapi.html}} 52 +\references{\url{https://www.kegg.jp/kegg/docs/keggapi.html}} 53 53  \author{Jianhua Zhang} 54 54   55 55  \seealso{\code{\link{browseURL}}} 56 56  \examples{ 57 - url <- mark.pathway.by.objects("path:eco00260", 58 - c("eco:b0002", "eco:c00263")) 59 - if(interactive()){ 60 - browseURL(url) 61 - } 62 - url <- color.pathway.by.objects("path:eco00260", 63 - c("eco:b0002", "eco:c00263"), 64 - c("#ff0000", "#00ff00"), c("#ffff00", "yellow")) 65 -  57 + url <- mark.pathway.by.objects( 58 + "path:eco00260", c("eco:b0002", "eco:c00263") 59 +) 60 +if(interactive()){ 61 + browseURL(url) 62 +} 63 +url <- color.pathway.by.objects( 64 + "path:eco00260", c("eco:b0002", "eco:c00263"), 65 + c("#ff0000", "#00ff00"), 66 + c("#ffff00", "yellow") 67 +) 66 68  } 67 69  \keyword{ datasets } 68 70 

#### progress on vignette

Dan Tenenbaum authored on 08/01/2013 00:19:14
Showing1 changed files
 ... ... @@ -40,7 +40,11 @@ color.pathway.by.objects(pathway.id, object.id.list, 40 40  } 41 41  \details{ 42 42  This function only returns the URL of the KEGG pathway diagram. Use 43 - the function \code{\link{browseURL}} to view the diagram 43 + the function \code{\link{browseURL}} to view the diagram. 44 + 45 + These functions are not part of the KEGG REST API; they are provided 46 + because they existed in \code{KEGGSOAP} and an alternative implementation 47 + was possible. 44 48  } 45 49  \value{ 46 50  This function returns a character string for the url

#### passes check

 ... ... @@ -45,7 +45,7 @@ color.pathway.by.objects(pathway.id, object.id.list, 45 45  \value{ 46 46  This function returns a character string for the url 47 47  } 48 -\references{\url{http://www.genome.jp/kegg/soap/doc/keggapi_manual.html}} 48 +\references{\url{http://www.kegg.jp/kegg/docs/keggapi.html}} 49 49  \author{Jianhua Zhang} 50 50   51 51  \seealso{\code{\link{browseURL}}}
 1 1 new file mode 100644 ... ... @@ -0,0 +1,64 @@ 1 +\name{mark.pathway.by.objects} 2 +\alias{mark.pathway.by.objects} 3 +\alias{color.pathway.by.objects} 4 + 5 +\title{Client-side interface to obtain an url for a KEGG pathway diagram 6 +with a given set of genes marked} 7 +\description{ 8 + Given a KEGG pathway id and a set of KEGG gene ids, the functions 9 + return the URL of a KEGG pathway diagram with the elements 10 + corresponding to the genes marked by red or specified color 11 +} 12 +\usage{ 13 +mark.pathway.by.objects(pathway.id, object.id.list) 14 +color.pathway.by.objects(pathway.id, object.id.list, 15 + fg.color.list, bg.color.list) 16 +} 17 + 18 +\arguments{ 19 + \item{pathway.id}{\code{pathway.id} a character string for a KEGG 20 + pathway id. KEGG pathway ids consist of the string path followed by 21 + a colon, a three-letter code for the organism of concern, and then 22 + a number (e. g. "path:eco00020"). The three-letter organism code 23 + consists of the first letter of the genus name and the first two 24 + letters of the species name of the scientific name of the organism 25 + of concern} 26 + \item{object.id.list}{\code{object.id.list} a vector of character 27 + strings for KEGG gene ids. KEGG gene ids normally consist of 28 + three letters followed by a column and then several numeric 29 + numbers. The three letters are from the first letter of the genus 30 + name and the first two letters of the species name of the scientific 31 + name of the organism of concern (e. g. hsa:111 for Homo Sapiens)} 32 + \item{fg.color.list}{\code{fg.color.list} a vector of two character 33 + strings to indicate the color for the text and border, respectively, 34 + of the objects in a pathway diagram. The strings can either be a 35 + color code linke \#ff0000 or letter link yellow} 36 + \item{bg.color.list}{\code{bg.color.list} a vector of character 37 + strings of the same length of \code{object.id.list} to indicate the 38 + background color of the objects in a pathway diagram. The strings 39 + can either be a color code like \#ff0000 or letter like yellow} 40 +} 41 +\details{ 42 + This function only returns the URL of the KEGG pathway diagram. Use 43 + the function \code{\link{browseURL}} to view the diagram 44 +} 45 +\value{ 46 + This function returns a character string for the url 47 +} 48 +\references{\url{http://www.genome.jp/kegg/soap/doc/keggapi_manual.html}} 49 +\author{Jianhua Zhang} 50 + 51 +\seealso{\code{\link{browseURL}}} 52 +\examples{ 53 + url <- mark.pathway.by.objects("path:eco00260", 54 + c("eco:b0002", "eco:c00263")) 55 + if(interactive()){ 56 + browseURL(url) 57 + } 58 + url <- color.pathway.by.objects("path:eco00260", 59 + c("eco:b0002", "eco:c00263"), 60 + c("#ff0000", "#00ff00"), c("#ffff00", "yellow")) 61 +  62 +} 63 +\keyword{ datasets } 64 +