update version 1.1.5

-Remove and replace Dependency cgdsr

-Updated the data file: hgnc2pfam

.Rbuildignore

@@ -17,3 +17,4 @@
 ^\.DS_Store$
 ^examples$
 ^R/proteinDomain.R$
+^LICENSE\.md$

.travis.yml

@@ -3,7 +3,7 @@ sudo: false
 cache: packages
 
 install:
-- R -e 'install.packages(c("jsonlite", "cgdsr", "stringr", "htmlwidgets", "knitr", "rmarkdown", "kableExtra", "shiny"))'
+- R -e 'install.packages(c("jsonlite", "cBioPortalData", "stringr", "htmlwidgets", "knitr", "rmarkdown", "kableExtra", "shiny"))'
 
 script:
 - R CMD build .

DESCRIPTION

@@ -1,22 +1,24 @@
 Package: g3viz
 Type: Package
 Title: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram
-Version: 1.1.3
+Version: 1.1.5
 Authors@R: c(
-    person("Xin", "Guo", email = "[email protected]", role = c("aut", "cre"))
+    person("Xin", "Guo", email = "[email protected]", role = c("aut","cre")),
+    person("Rener", "Zhang", email = "[email protected]", role = c("ctb"))
     )
 Maintainer: Xin Guo <[email protected]>
-Description: R interface for 'g3-lollipop' JavaScript library.
-    Visualize genetic mutation data using an interactive lollipop diagram in RStudio or your browser.
+Description: Interface for 'g3-lollipop' JavaScript library.
+    Visualize genetic mutation data using an interactive lollipop diagram in Studio or your browser.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends:
-    R (>= 3.0.0)
+    R (>= 3.5.0)
+biocViews:
 Imports:
     jsonlite,
-    cgdsr,
     stringr,
+    cBioPortalData,
     htmlwidgets
 Suggests:
     shiny (>= 1.0.0),
@@ -25,5 +27,5 @@ Suggests:
     kableExtra
 URL: https://github.com/G3viz/g3viz
 BugReports: https://github.com/G3viz/g3viz/issues
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 VignetteBuilder: knitr

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2018-2019
+YEAR: 2022
 COPYRIGHT HOLDER: Xin Guo <[email protected]>

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2022 g3viz authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -13,10 +13,11 @@ export(parseProteinChange)
 export(readMAF)
 export(renderG3Lollipop)
 export(uniprot2pfam)
-importFrom(cgdsr,CGDS)
-importFrom(cgdsr,getCaseLists)
-importFrom(cgdsr,getGeneticProfiles)
-importFrom(cgdsr,getMutationData)
+importFrom(cBioPortalData,cBioPortal)
+importFrom(cBioPortalData,getDataByGenes)
+importFrom(cBioPortalData,molecularProfiles)
+importFrom(cBioPortalData,sampleLists)
+importFrom(cBioPortalData,samplesInSampleLists)
 importFrom(htmlwidgets,shinyRenderWidget)
 importFrom(htmlwidgets,shinyWidgetOutput)
 importFrom(jsonlite,toJSON)

NEWS.md

@@ -1,3 +1,8 @@
+## Version 1.15 (2022/06/30)
+  - Updated `hgnc2pfam.df.rda` data
+  - Remove cgdsr dependencies; add cBioPortalData as the substitution
+  - Updated getMutationsFromCbioportal.R ([issue 16](https://github.com/G3viz/g3viz/issues/16)).
+
 ## Version 1.1.3 (2020/08/24)
   - Updated Pfam version 33.1 (date: 2020-08-24)
   - Updated UniProt (date: 2020-08-24)

R/g3Lollipop.R

@@ -29,6 +29,8 @@
 #'   two built-in styles, \emph{blue} or \emph{gray}. Default \code{NA},
 #'   indicating browser default.
 #' @param output.filename Specify output file name.
+#' @return lollipop diagram for the given mutation data. The chart is interactive
+#'   within either Shiny applications or Rmd documents under the bindings.
 #'
 #' @examples
 #'
@@ -170,6 +172,8 @@ g3Lollipop <- function(mutation.dat,
 #' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
 #'   is useful if you want to save an expression in a variable.
 #'
+#' @return No value returned. It is the binding which enables interactive functions
+#'   within Shiny applications and Rmd documents.
 #' @name g3Lollipop-shiny
 #'
 #' @importFrom htmlwidgets shinyWidgetOutput

R/getMutationsFromCbioportal.R

@@ -9,37 +9,31 @@
 #' @param mutation.type.to.class.df mapping table from mutation type to class.
 #'   See \code{\link{mapMutationTypeToMutationClass}} for details. Default
 #'   \code{NA}, which indicates to use default mappings.
-#' @param cgds.url the URL for the public CGDS server (Cancer Genomic Data
-#'   Server). Default is \url{http://www.cbioportal.org/}. Check
-#'   \emph{cgdsr} R-package for details.
-#' @param test.cgds if test CGDS connection.  Default is \code{FALSE}
 #' @examples
 #' \dontrun{
 #' # Usage:
-#' # Connection to CGDS (Cange Genomic Data Server). Internet access required.
-#' # Note: this may need more than 10 seconds, and sometimes it may fail.
-#' library(cgdsr)
-#' cgds <- CGDS("http://www.cbioportal.org/")
-#'
-#' # test if connection is OK (warning: sometimes it may fail)
-#' test(cgds)
+#' # cBioPortalData has officially replaced the defunct cgdsr.
+#' # Search online for cgdsrMigration.html if interested.
+#' library(cBioPortalData)
+#' cbio <- cBioPortal()
 #'
 #' # list all studies of cBioPortal
-#' all.studies <- getCancerStudies(cgds)
+#' all.studies <- getStudies(cbio, buildReport = FALSE)
 #'
 #' # First, select a cancer study that contains mutation data set ("caner_study_id")
 #' # then, query genomic mutation data using a HGNC gene symbol,
 #' # for example
 #' mutation.dat <- getMutationsFromCbioportal("msk_impact_2017", "TP53")
 #' mutation.dat <- getMutationsFromCbioportal("all_stjude_2016", "TP53")
 #' }
-#' @importFrom cgdsr CGDS getGeneticProfiles getCaseLists getMutationData
+#' @importFrom cBioPortalData cBioPortal molecularProfiles sampleLists getDataByGenes
+#'             samplesInSampleLists
 #' @importFrom utils write.table
 #'
 #' @return a data frame with columns
 #'   \describe{
 #'       \item{Hugo_Symbol}{Hugo gene symbol}
-#'       \item{Protein_Change}{Protein change information (cBioprotal uses \emph{HGVSp} format)}
+#'       \item{Protein_Change}{Protein change information (cBioportal uses \emph{HGVSp} format)}
 #'       \item{Sample_ID}{Sample ID}
 #'       \item{Mutation_Type}{mutation type, aka, variant classification.}
 #'       \item{Chromosome}{chromosome}
@@ -55,52 +49,53 @@
 getMutationsFromCbioportal <- function(study.id,
                                        gene.symbol,
                                        output.file = NA,
-                                       mutation.type.to.class.df = NA,
-                                       cgds.url = "http://www.cbioportal.org/",
-                                       test.cgds = FALSE){
-  # =============================
-  # define mutation columns
-  aa.pos.col <- "AA_Position"
-  mutation.class.col <- "Mutation_Class"
+                                       mutation.type.to.class.df = NA){
 
   # ========================
-  # cgds server
-  cgds <- cgdsr::CGDS(cgds.url)
-
-  # ========================
-  # test cgds
-  if(test.cgds){
-    cgdsr::test(cgds)
-  }
+  # server
+  cbio <- cBioPortal()
 
   # ========================
   # get study information
-  genetic.profiles <- getGeneticProfiles(cgds, study.id)
+  genetic.profiles <- molecularProfiles(cbio,studyId = study.id)
   message("Found study ", study.id)
 
   # ========================
-  # check if mutation informaiton is available in the study
-  profile.col <- "genetic_profile_id"
-  mutation.idx <- grep(pattern = 'mutations$', x = genetic.profiles[, profile.col], fixed = FALSE)
+  # check if mutation information is available in the study
+  profile.col <- "molecularProfileId"
+  mutation.idx <- grep(pattern = 'mutations$', x = genetic.profiles$molecularProfileId, fixed = FALSE)
   if(is.integer(mutation.idx) && length(mutation.idx) == 0L){
     stop("Can not find mutation information in ", study.id, " study")
   }
-  mutation.profile <- genetic.profiles[mutation.idx, profile.col]
+  mutation.profile <- genetic.profiles$molecularProfileId[mutation.idx]
   message("Found mutation data set ", mutation.profile)
 
   # ========================
-  # get case list
-  case.list.details <- getCaseLists(cgds, study.id)[mutation.idx, ]
-  mutation.case.list.id <- case.list.details$case_list_id
-  num.case <- length(strsplit(case.list.details$case_ids, " ")[[1]])
+
+  case.list.details <- sampleLists(cbio, study.id)
+
+  mutation.case.list.id <- case.list.details$sampleListId
+
+  mutation.case.list.all <- mutation.case.list.id[grep(pattern = '_sequenced$',x = mutation.case.list.id)]
+  num.case <- length(samplesInSampleLists(cbio,mutation.case.list.id)[[mutation.case.list.all]])
   message(num.case, " cases in this study")
 
-  extended.mutation.df <- getMutationData(cgds, mutation.case.list.id, mutation.profile, gene.symbol)
+  ### Download mutation data on certain gene from study
+  df <- getDataByGenes(
+        cbio,
+        studyId = study.id,
+        genes = gene.symbol,
+        by = "hugoGeneSymbol",
+        molecularProfileIds = mutation.profile
+      )[[1]]
+
+  extended.mutation.df <- cbind(rep(gene.symbol,nrow(df)),df)
+  colnames(extended.mutation.df) <- c("gene_symbol",colnames(df))
   # =========================
   # parse mutation data columns
-  required.colnames <- c("gene_symbol", "amino_acid_change", "case_id", "mutation_type",
-                         "chr", "start_position", "end_position",
-                         "reference_allele", "variant_allele")
+  required.colnames <- c("gene_symbol", "proteinChange", "sampleId", "mutationType",
+                         "chr", "startPosition", "endPosition",
+                         "referenceAllele", "variantAllele")
 
   mapped.colnames <- c("Hugo_Symbol", "Protein_Change", "Sample_ID", "Mutation_Type",
                        "Chromosome", "Start_Position", "End_Position",
@@ -117,17 +112,18 @@ getMutationsFromCbioportal <- function(study.id,
   mutation.df <- extended.mutation.df[, required.colnames]
   colnames(mutation.df) <- mapped.colnames
 
+
   # =============================
   # map from mutation type to mutation class
-  mutation.df[, mutation.class.col] <- mapMutationTypeToMutationClass(mutation.df[, "Mutation_Type"],
+  mutation.df[, "Mutation_Class"] <- mapMutationTypeToMutationClass(mutation.df[, "Mutation_Type"],
                                                                       mutation.type.to.class.df)
 
   # =============================
   # parse amino acid position
-  mutation.df[, aa.pos.col] <- parseProteinChange(mutation.df[, "Protein_Change"],
-                                                  mutation.df[, mutation.class.col])
+  mutation.df[, "AA_Position"] <- parseProteinChange(mutation.df[, "Protein_Change"],
+                                                  mutation.df[, "Mutation_Class"])
 
-  mutation.df <- mutation.df[order(mutation.df[, aa.pos.col],
+  mutation.df <- mutation.df[order(mutation.df[, "AA_Position"],
                                    mutation.df[, "Protein_Change"], decreasing = FALSE), ]
 
   if(!is.na(output.file)){

R/parseProteinChange.R

@@ -27,7 +27,7 @@ parseProteinChange <- function(protein.change.vec, mutation.class.vec) {
 
     if(!(is.na(d.mc) || d.mc == "Other" || d.mc == "")){
       # extract the first numeric value
-      aa.pos.vec[idx] = as.numeric(str_extract_all(d.pc, "[0-9]+")[[1]])[1]
+      aa.pos.vec[idx] <- as.numeric(str_extract_all(d.pc, "[0-9]+")[[1]])[1]
     }
     # cat(d.pc, " ==> ", aa.pos.vec[idx], "\n")
   }

R/uniprot2pfam.R

@@ -1,6 +1,6 @@
 #' From UniProt ID to Pfam-A domain composition
 #'
-#' @description Map from UniProt ID to Pfam-A domain compostion.
+#' @description Map from UniProt ID to Pfam-A domain composition.
 #' @param uniprot.id UniProt ID
 #' @return a data frame with columns
 #' \itemize{

R/zzz.R

@@ -2,7 +2,7 @@
   packageStartupMessage(
 "g3viz: visualizing gene/genome/gentics data for fun.
   - Pfam (v33.1)
-  - UniProt (date: 2020/08/24)\n
+  - UniProt (date: 2022/07/01)\n
 Any questions, please send emails to <[email protected]> or post on GitHub <https://github.com/G3viz/g3viz/issues>."
     )
 }

README.md

@@ -1,6 +1,6 @@
 # <a name="top"></a>G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram
 
-  **Date: 2022-08-19**
+  **Date: 2022-06-30**
 
   [![Build Status](https://travis-ci.org/G3viz/g3viz.svg?branch=master)](https://travis-ci.org/G3viz/g3viz)
   [![CRAN_version](http://www.r-pkg.org/badges/version/g3viz)](https://cran.r-project.org/package=g3viz)
@@ -48,12 +48,7 @@ Guo, X., *et al*. (2020). G3viz: an R package to interactively visualize genetic
 
 ## What's new
 
-1.1.3 
-  - [x] Updated Pfam version 33.1 (date: 2020-08-24)
-  - [x] Updated UniProt (date: 2020-08-24)
-  - [x] add "prepare_data" folder to instruct how to create `hgnc2pfam.df.rda` data
-
-1.1.5
+1.1.5 
   - [x] Updated getMutationsFromCbioportal (date: 2022-06-23)
   - [x] Remove Dependency cgdsr; Add Dependency cBioPortalData (date: 2022-06-23)
   - [x] Updated `hgnc2pfam.df.rda` (date: 2022-06-24)