version 0.4

DESCRIPTION

@@ -1,12 +1,13 @@
-Package: g3viz
+Package: g3lollipop
 Type: Package
-Title: Visualize Genomic Mutation Data Using an Interactive Lollipop Diagram
-Version: 0.1.4
+Title: Visualize Genomic Mutation Data via an Interactive Lollipop Diagram
+Version: 0.3
 Authors@R: c(
-    person("Xin", "Guo", , "[email protected]", c("aut", "cre"))
+    person("Xin", "Guo", email = "[email protected]", role = c("aut", "cre"))
     )
 Maintainer: Xin Guo <[email protected]>
-Description: R interface for 'g3viz' JavaScript library. Using an interactive lollipop diagram to visualize genomic mutation data in a web browser.
+Description: R interface for 'g3viz' JavaScript library.
+    Visualize Genomic Mutation Data Using a rich interactive lollipop diagram in Rstudio or your browser.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -21,7 +22,7 @@ Suggests:
     shiny (>= 1.0.0),
     knitr,
     rmarkdown
-URL: https://github.com/G3js/lollipopR
-BugReports: https://github.com/G3js/lollipopR/issues
+URL: https://github.com/G3viz/g3lollipop
+BugReports: https://github.com/G3viz/g3lollipop/issues
 RoxygenNote: 6.1.1
 VignetteBuilder: knitr

R/getMutationsFromCbioportal.R

@@ -6,14 +6,18 @@
 #' @param gene.symbol HGNC gene symbol.
 #' @param output.file if specified, output to a file in \emph{CSV} format. Default is \code{NA}.
 #' @param mutation.type.to.class.df mapping table from mutation type to class.
+#' @param cgds.url the URL for the public CGDS server, refer to
+#' @param test.cbioportal test CGDS connection
 #' See \code{\link{mapMutationTypeToMutationClass}} for details.
 #' Default \code{NA}, which indicates to use default mappings.
 #' @examples
 #' \dontrun{
 #' # Note: internet access required.  May need more than 10 seconds.
 #' # list all studies of cBioPortal
 #' library(cgdsr)
-#' cgds <- CGDS("http://www.cbioportal.org/public-portal/")
+#' cgds <- CGDS("http://www.cbioportal.org/")
+#' # test if connection is OK (warning: sometimes it may fail)
+#' test(cgds)
 #' all.studies <- getCancerStudies(cgds)
 #'
 #' # pick a "caner_study_id" (contain a mutation data set)
@@ -42,7 +46,9 @@
 getMutationsFromCbioportal <- function(study.id,
                                        gene.symbol,
                                        output.file = NA,
-                                       mutation.type.to.class.df = NA){
+                                       mutation.type.to.class.df = NA,
+                                       cbioportal.url = "http://www.cbioportal.org/",
+                                       test.cbioportal = FALSE){
   # =============================
   # define mutation columns
   aa.pos.col <- "AA_Position"

vignettes/introduction.Rmd

@@ -3,7 +3,7 @@ title: "G3viz: Interactively visualize genomic data in a web browser"
 date: "2018-08-30"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteIndexEntry{G3viz: interactively visualize genomic data in a web browser}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---