diff --git a/DESCRIPTION b/DESCRIPTION index 9714992..2b6d9ce 100644 --- a/DESCRIPTION +++ b/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", , "phoeguo@gmail.com", c("aut", "cre")) + person("Xin", "Guo", email = "phoeguo@gmail.com", role = c("aut", "cre")) ) Maintainer: Xin Guo -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 diff --git a/R/getMutationsFromCbioportal.R b/R/getMutationsFromCbioportal.R index d017cba..95cb952 100644 --- a/R/getMutationsFromCbioportal.R +++ b/R/getMutationsFromCbioportal.R @@ -6,6 +6,8 @@ #' @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 @@ -13,7 +15,9 @@ #' # 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" diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd index df65a07..ead80d5 100644 --- a/vignettes/introduction.Rmd +++ b/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} ---