Merging master

From: Thomas Dybdal Pedersen <thomasp85@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PanVizGenerator@114380 bc3139a8-67e5-0310-9ffc-ced21a209358

.gitignore

@@ -0,0 +1,6 @@
+.Rproj.user
+.Rhistory
+.RData
+*.Rproj
+.Rbuildignore
+inst/shinyapps/

.travis.yml

@@ -0,0 +1,11 @@
+# Sample .travis.yml for R projects
+
+language: r
+warnings_are_errors: true
+sudo: required
+bioc_required: true
+r_github_packages:
+  - thomasp85/FindMyFriends
+  - jimhester/covr
+after_success:
+  - Rscript -e 'library(covr);codecov()'

DESCRIPTION

@@ -1,23 +1,43 @@
-Package: PanVizGenerator
-Type: Package
-Title: Generate PanViz visualisations from your pangenome
-Version: 0.99.0
-Date: 2015-10-30
-Author: Thomas Lin Pedersen
-Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
-Description: PanViz is a JavaScript based visualisation tool for functionaly annotated
-          pangenomes. PanVizGenerator is a companion for PanViz that facilitates the
-          necessary data preprocessing step necessary to create a working PanViz
-          visualization. The output is fully self-contained so the recipient of the
-          visualization does not need R or PanVizGenerator installed.
-License: GPL (>= 2)
-URL: https://github.com/thomasp85/PanVizGenerator
-BugReports: https://github.com/thomasp85/PanVizGenerator/issues
-biocViews: ComparativeGenomics, GUI, Visualization
-Depends: methods
-Imports: shiny, tools, jsonlite, pcaMethods, FindMyFriends, igraph, stats, utils
-VignetteBuilder: knitr
-Suggests: BiocStyle, knitr, rmarkdown, testthat, digest
-Collate: 'GO.R' 'aaa.R' 'IO.R' 'panviz.R' 'shinyStuff.R' 'zzz.R'
-RoxygenNote: 5.0.0.9000
-NeedsCompilation: no
+Package: PanVizGenerator
+Type: Package
+Title: Generate PanViz visualisations from your pangenome
+Version: 0.99.1
+Date: 2016-03-08
+Author: Thomas Lin Pedersen
+Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
+Description: PanViz is a JavaScript based visualisation tool for functionaly
+    annotated pangenomes. PanVizGenerator is a companion for PanViz that
+    facilitates the necessary data preprocessing step necessary to create a
+    working PanViz visualization. The output is fully self-contained so the
+    recipient of the visualization does not need R or PanVizGenerator installed.
+License: GPL (>= 2)
+URL: https://github.com/thomasp85/PanVizGenerator
+BugReports: https://github.com/thomasp85/PanVizGenerator/issues
+biocViews: ComparativeGenomics, GUI, Visualization
+Depends:
+    methods
+Imports:
+    shiny,
+    tools,
+    jsonlite,
+    pcaMethods,
+    FindMyFriends,
+    igraph,
+    stats,
+    utils
+VignetteBuilder: knitr
+Suggests:
+    BiocStyle,
+    knitr,
+    rmarkdown,
+    testthat,
+    digest
+Collate:
+    'GO.R'
+    'aaa.R'
+    'IO.R'
+    'panviz.R'
+    'shinyStuff.R'
+    'zzz.R'
+RoxygenNote: 5.0.1
+

NAMESPACE

@@ -7,7 +7,6 @@ import(methods)
 importClassesFrom(FindMyFriends,pgVirtual)
 importFrom(FindMyFriends,groupInfo)
 importFrom(FindMyFriends,groupNames)
-importFrom(FindMyFriends,pgMatrix)
 importFrom(igraph,"V<-")
 importFrom(igraph,"vertex_attr<-")
 importFrom(igraph,E)

NEWS

@@ -1,7 +1,7 @@
 Version 0.99.0
 ________________________________________________________________________________
 * Submission for Bioconductor
-* Added Vignette
+* Added vignette
 * Added panviz method for use of functionality in R (instead of just shiny)
 * Make gene ontology a subsequent download instead of bundle with package
 * Check usability of current GO before building PanViz

R/panviz.R

@@ -164,7 +164,7 @@ setMethod(
 #' @describeIn panviz Method for pgVirtual subclasses from FindMyFriends
 #' 
 #' @importClassesFrom FindMyFriends pgVirtual
-#' @importFrom FindMyFriends groupInfo pgMatrix groupNames
+#' @importFrom FindMyFriends groupInfo groupNames
 #' 
 setMethod(
     'panviz', 'pgVirtual',
@@ -176,7 +176,7 @@ setMethod(
         }
         name <- ifelse(is.na(gInfo$description), groupNames(object), 
                        gInfo$description)
-        mat <- pgMatrix(object)
+        mat <- as(object, 'matrix')
         panviz(mat, name = name, go = gInfo$GO, ec = gInfo$EC, 
                location = location, consolidate = consolidate, 
                showcase = showcase, ...)