version 1.0.0

.gitignore

@@ -4,7 +4,7 @@ inst/doc
 .RData
 .Ruserdata
 packrat/lib*/
-data-raw/temp/
+data-raw/
 R/temp/
 inst/backup/
 inst/extdata/backup/

DESCRIPTION

@@ -1,18 +1,18 @@
-Package: g3lollipop
+Package: g3viz
 Type: Package
-Title: Visualize Genomic Mutation Data via an Interactive Lollipop Diagram
-Version: 0.3
+Title: Visualize Genomic Mutation Data using a Rich Interactive Lollipop Diagram
+Version: 1.0.0
 Authors@R: c(
     person("Xin", "Guo", email = "[email protected]", role = c("aut", "cre"))
     )
 Maintainer: Xin Guo <[email protected]>
-Description: R interface for 'g3viz' JavaScript library.
-    Visualize Genomic Mutation Data Using a rich interactive lollipop diagram in Rstudio or your browser.
+Description: R interface for 'g3lollipop' 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
 Depends:
-    R (>= 3.0.2)
+    R (>= 3.0.0)
 Imports:
     jsonlite,
     cgdsr,
@@ -22,7 +22,7 @@ Suggests:
     shiny (>= 1.0.0),
     knitr,
     rmarkdown
-URL: https://github.com/G3viz/g3lollipop
-BugReports: https://github.com/G3viz/g3lollipop/issues
+URL: https://github.com/G3viz/g3viz
+BugReports: https://github.com/G3viz/g3viz/issues
 RoxygenNote: 6.1.1
 VignetteBuilder: knitr

R/getMutationsFromCbioportal.R

@@ -6,22 +6,29 @@
 #' @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.
+#' @param cgds.url the URL for the public CGDS server (Cancer Genomic Data Server).
+#' Default is \url{http://www.cbioportal.org/}.
+#' Check \href{https://cran.r-project.org/web/packages/cgdsr/}{cgdsr} package for details.
+#' @param test.cgds if test CGDS connection.  Default is \code{FALSE}
 #' @examples
 #' \dontrun{
-#' # Note: internet access required.  May need more than 10 seconds.
-#' # list all studies of cBioPortal
+#' # 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)
+#'
+#' # list all studies of cBioPortal
 #' all.studies <- getCancerStudies(cgds)
 #'
-#' # pick a "caner_study_id" (contain a mutation data set)
-#' # pick a primary HGNC gene symbol to query
+#' # 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")
 #' }
@@ -47,16 +54,22 @@ getMutationsFromCbioportal <- function(study.id,
                                        gene.symbol,
                                        output.file = NA,
                                        mutation.type.to.class.df = NA,
-                                       cbioportal.url = "http://www.cbioportal.org/",
-                                       test.cbioportal = FALSE){
+                                       cgds.url = "http://www.cbioportal.org/",
+                                       test.cgds = FALSE){
   # =============================
   # define mutation columns
   aa.pos.col <- "AA_Position"
   mutation.class.col <- "Mutation_Class"
 
   # ========================
   # cgds server
-  cgds <- CGDS("http://www.cbioportal.org/public-portal/")
+  cgds <- cgdsr::CGDS(cgds.url)
+
+  # ========================
+  # test cgds
+  if(test.cgds){
+    cgdsr::test(cgds)
+  }
 
   # ========================
   # get study information

R/mapMutationTypeToMutationClass.R

@@ -17,35 +17,38 @@
 #'   }
 #'   \item Truncating
 #'     \itemize{
-#'       \item \emph{Frame_Shift_Ins} --- insertion that moves the coding sequence out of frame.
+#'       \item \emph{Frame_Shift} --- moves the coding sequence out of frame.
+#'             However, insertion or deletion can not be determined.
 #'             See \url{https://en.wikipedia.org/wiki/Frameshift_mutation}.
-#'       \item \emph{Frame_Shift_Del} --- deletion that moves the coding sequence out of frame.
+#'       \item \emph{Frame_Shift_Ins} --- an insertion that moves the coding sequence out of frame.
 #'             See \url{https://en.wikipedia.org/wiki/Frameshift_mutation}.
-#'       \item \emph{Nonsense_Mutation} --- a premature stop codon is created by the variant.
+#'       \item \emph{Frame_Shift_Del} --- a deletion that moves the coding sequence out of frame.
+#'             See \url{https://en.wikipedia.org/wiki/Frameshift_mutation}.
+#'       \item \emph{Nonsense_Mutation} --- a premature stop codon that is created by the variant.
 #'             See \url{https://en.wikipedia.org/wiki/Nonsense_mutation}.
-#'       \item \emph{Nonstop_Mutation} --- variant removes stop codon.
-#'       \item \emph{Splice_Site} --- the variant is within two bases of a splice site.
-#'       \item \emph{Splice_Region} --- the variant is within splice region.
+#'       \item \emph{Nonstop_Mutation} --- a variant that removes stop codon.
+#'       \item \emph{Splice_Site} --- a variant that is within two bases of a splice site.
+#'       \item \emph{Splice_Region} --- a variant that is within splice region.
 #'  }
 #'  \item Other
 #'  \itemize{
-#'     \item \emph{5'UTR} --- variant is on the 5'UTR for the chosen transcript
-#'     \item \emph{3'UTR} --- variant is on the 3'UTR for the chosen transcript
-#'     \item \emph{5'Flank} --- the variant is upstream of the chosen transcript (within 3kb)
-#'     \item \emph{3'Flank} --- the variant is downstream of the chosen transcript (within 3kb)
-#'     \item \emph{Fusion} --- gene fusion
-#'     \item \emph{IGR} --- intergenic region. Does not overlap any transcript.
-#'     \item \emph{Intron} --- variant lies between exons within the bounds of the chosen transcript.
-#'     \item \emph{Translation_Start_Site} --- variant in translation start site.
-#'     \item \emph{De_novo_Start_InFrame} --- New start codon is created by the given variant using the chosen transcript.
+#'     \item \emph{5'UTR} --- a variant that is on the 5'UTR for the chosen transcript.
+#'     \item \emph{3'UTR} --- a variant that is on the 3'UTR for the chosen transcript.
+#'     \item \emph{5'Flank} --- a variant that is upstream of the chosen transcript (generally within 3kb).
+#'     \item \emph{3'Flank} --- a variant that is downstream of the chosen transcript (generally within 3kb).
+#'     \item \emph{Fusion} --- a gene fusion.
+#'     \item \emph{IGR} --- an intergenic region. Does not overlap any transcript.
+#'     \item \emph{Intron} --- a variant that lies between exons within the bounds of the chosen transcript.
+#'     \item \emph{Translation_Start_Site} --- a variant that is in translation start site.
+#'     \item \emph{De_novo_Start_InFrame} --- a novel start codon that is created by the given variant using the chosen transcript.
 #'           However, it is in frame relative to the coded protein.
-#'     \item \emph{De_novo_Start_OutOfFrame} --- New start codon is created by the given variant using the chosen transcript.
+#'     \item \emph{De_novo_Start_OutOfFrame} --- a novel start codon that is created by the given variant using the chosen transcript.
 #'           However, it is out of frame relative to the coded protein.
-#'     \item \emph{Start_Codon_SNP} --- point mutation that overlaps the start codon.
-#'     \item \emph{Start_Codon_Ins} --- insertion that overlaps the start codon.
-#'     \item \emph{Start_Codon_Del} --- selection that overlaps the start codon.
-#'     \item \emph{RNA} --- variant lies on one of the RNA transcripts.
-#'     \item \emph{lincRNA} --- variant lies on one of the lincRNAs.
+#'     \item \emph{Start_Codon_SNP} --- a point mutation that overlaps the start codon.
+#'     \item \emph{Start_Codon_Ins} --- an insertion that overlaps the start codon.
+#'     \item \emph{Start_Codon_Del} --- a deletion that overlaps the start codon.
+#'     \item \emph{RNA} --- a variant that lies on one of the RNA transcripts.
+#'     \item \emph{lincRNA} --- a variant that lies on one of the lincRNAs.
 #'     \item \emph{Unknown} --- Unknown
 #'   }
 #' }
@@ -83,5 +86,3 @@ mapMutationTypeToMutationClass <- function(mutation.type.vec,
   mutation.class.vec <- Map.df[match(mutation.type.vec, Map.df$Mutation_Type), "Mutation_Class"]
   mutation.class.vec
 }
-
-

data-raw/g3viz-package.R

@@ -1,4 +1,3 @@
 .onLoad <- function(libname, pkgname){
   packageStartupMessage("G3viz: visualize gene/genome/genetics.")
-#  data(list = c("hgnc2pfam.df", "mutation.table.df"), package = pkgname, envir = parent.env(enviroment()))
 }

g3viz.Rproj

@@ -18,4 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette