bug fix #3 and docs

egonw · Sep 9, 2018 · afcccba · afcccba
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,4 +22,4 @@ LazyLoad: yes
 biocViews: Visualization, GraphAndNetwork, ThirdPartyClient, Network, Metabolomics
 NeedsCompilation: no
 VignetteBuilder: knitr
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
diff --git a/R/downloadPathwayArchive.R b/R/downloadPathwayArchive.R
@@ -2,23 +2,26 @@
 #' @title Download Pathway Archive
 #'
 #' @description Access the monthly archives of pathway content from WikiPathways.
-#' @details If you specify an archive date, organism and format, then the archive file
-#' will be downloaded. Otherwise, the archive will be opened in a tab in your
+#' @details If you do not specify an organism, then an archive file
+#' will not be downloaded. Rather, the archive will be opened in a tab in your
 #' default browser.
 #' @param date (optional) The timestamp for a monthly release (e.g., 20171010) 
 #' or "current" (default) for latest release.
 #' @param organism (optional) A particular species. See \link{listOrganisms}. 
 #' @param format (optional) Either gpml (default), gmt or svg.
-#' @return Downloaded file or tab in default browser
+#' @param destpath (optional) Destination path for file to be downloaded to.
+#' Default is current workding directory.
+#' @return Filename of downloaded file or an opened tab in default browser
 #' @examples \donttest{
-#' downloadPathwayArchive()
-#' downloadPathwayArchive(format="gmt")
-#' downloadPathwayArchive(date="20171010", format="svg")
-#' downloadPathwayArchive(date="20171010", organism="Mus musculus", format="svg")
+#' downloadPathwayArchive()  ## open in browser
+#' downloadPathwayArchive(format="gmt")  ## open in browser
+#' downloadPathwayArchive(date="20171010", format="svg")  ## open in browser
+#' downloadPathwayArchive(date="20171010", organism="Mus musculus", format="svg")  ## download file
+#' downloadPathwayArchive(organism="Mus musculus")  ## download file
 #' }
 #' @export
 #' @importFrom utils browseURL download.file
-downloadPathwayArchive <- function(date='current',organism = NULL, format=c('gpml', 'gmt', 'svg')){
+downloadPathwayArchive <- function(date='current',organism=NULL, format=c('gpml', 'gmt', 'svg'), destpath='./'){
     #get validated format
     format <- match.arg(format)
 
@@ -34,14 +37,21 @@ downloadPathwayArchive <- function(date='current',organism = NULL, format=c('gpm
             stop('The organism must match the list of supported organisms, see listOrganisms()')
 
     #download specific file, or...
-    if (!is.null(organism) && date != 'current'){
-        ext <- ".zip"
-        if (format == 'gmt')
-            ext <- ".gmt"
-        filename <- paste0(paste('wikipathways',date,format,sub("\\s","_",organism),sep="-"), ext)
+    if (!is.null(organism)){
+        if (date == 'current'){ #determine filename
+            curr.files <- readHTMLTable(paste0('http://data.wikipathways.org/current/',format))[[1]]$Filename
+            filename <- grep(sub("\\s","_",organism), curr.files, value=TRUE)
+            if (length(filename) == 0)
+                stop ('Could not find a file matching your specifications. Try browsing http://data.wikipathways.org.')
+        } else { #construct filename
+            ext <- ".zip"
+            if (format == 'gmt')
+                ext <- ".gmt"
+            filename <- paste0(paste('wikipathways',date,format,sub("\\s","_",organism),sep="-"), ext)
+        }
         url <- paste('http://data.wikipathways.org',date, format, filename, sep="/")
-        download.file(url, filename, 'wget')
-
+        download.file(url, paste(destpath,filename,sep='/'), 'auto')
+        return(filename)
     } else { #...just open browser
         browseURL(paste('http://data.wikipathways.org',date, format ,sep="/"))
     }    

diff --git a/man/downloadPathwayArchive.Rd b/man/downloadPathwayArchive.Rd
diff --git a/man/getColoredPathway.Rd b/man/getColoredPathway.Rd
diff --git a/vignettes/Overview.Rmd b/vignettes/Overview.Rmd
@@ -6,6 +6,8 @@ date: "`r Sys.Date()`"
 output: 
   BiocStyle::html_document:
     toc_float: true
+#  pdf_document:
+#    toc: true 
 vignette: >
   %\VignetteIndexEntry{1. Overview}
   %\VignetteEngine{knitr::rmarkdown}
@@ -154,6 +156,24 @@ And, as you may have suspected from the function name, you can also add color to
 
 This will produce an svg image of the pathway with the ACE gene highlighted by color.
 
+WikiPathways also provides a monthly data release archived at http://data.wikipathways.org. The archive includes GPML, GMT and SVG collections by organism and timestamped. There's an R function for grabbing files from the archive...
+
+```{r}
+    downloadPathwayArchive()
+```
+
+This will simply open the archive in your default browser so you can look around (in case you don't know what you are looking for). By default, it opens to the latest collection of GPML files.  However, if you provide an organism, then it will download that file to your current working directory or specified **destpath**. For example, here's how you'd get the latest GMT file for mouse:
+
+```{r}
+    downloadPathwayArchive(organism="Mus musculus", format="gmt")
+```
+
+And if you might want to specify an archive date so that you can easily share and reproduce your script at any time in the future and get the same result. Remember, new pathways are being added to WikiPathways every month and existing pathways are improved continuously!
+
+```{r}
+    downloadPathwayArchive(date="20171010", organism="Mus musculus", format="gmt")
+```
+
 # Wrapping up
 
 That's an overview of the **rWikiPathways** package. Check out other vignettes and the complete list of package functions:

diff --git a/vignettes/rWikiPathways-and-BridgeDbR.Rmd b/vignettes/rWikiPathways-and-BridgeDbR.Rmd
@@ -6,18 +6,12 @@ date: "`r Sys.Date()`"
 output: 
   BiocStyle::html_document:
     toc_float: true
+#  pdf_document:
+#    toc: true 
 vignette: >
   %\VignetteIndexEntry{2. rWikiPathways and BridgeDbR}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
-bibliography: tutorial.bib
-csl: biomed-central.csl
-references:
-- id: dummy
-  title: no title
-  author:
-  - family: noname
-    given: noname
 ---
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(

diff --git a/vignettes/rWikiPathways-and-RCy3.Rmd b/vignettes/rWikiPathways-and-RCy3.Rmd
@@ -6,18 +6,12 @@ date: "`r Sys.Date()`"
 output: 
   BiocStyle::html_document:
     toc_float: true
+#  pdf_document:
+#    toc: true 
 vignette: >
   %\VignetteIndexEntry{3. rWikiPathways and RCy3}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
-bibliography: tutorial.bib
-csl: biomed-central.csl
-references:
-- id: dummy
-  title: no title
-  author:
-  - family: noname
-    given: noname
 ---
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(