Improve function documentation and add functions for get/setting spec…

…ies and assembly version of a data group, closes #88

R/begin.R

@@ -51,27 +51,53 @@ getInclusionLevels <- reactive(getCategoryData()[["Inclusion levels"]])
 #' @param sep Character to separate identifiers
 getGlobal <- function(..., sep="_") sharedData[[paste(..., sep=sep)]]
 
-#' Get table of differential analyses
+#' Get the table of differential analyses of a data category
 #' @note Needs to be called inside reactive function
-#' @param category Character: data category (e.g. "Carcinoma 2016")
+#' 
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
 #' 
 #' @return Data frame of differential analyses
 getDifferentialAnalyses <- function(category = getCategory())
     getGlobal(category, "differentialAnalyses")
 
+#' Get the species of a data category
+#' @note Needs to be called inside reactive function
+#' 
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
+#' 
+#' @return Character value with the species
+getSpecies <- function(category = getCategory())
+    getGlobal(category, "species")
+
+#' Get the assembly version of a data category
+#' @note Needs to be called inside reactive function
+#' 
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
+#' 
+#' @return Character value with the assembly version
+getAssemblyVersion <- function(category = getCategory())
+    getGlobal(category, "assemblyVersion")
+
 #' Get groups from a given data type
 #' @note Needs to be called inside reactive function
+#' 
 #' @param dataset Character: data set (e.g. "Clinical data")
-#' @param category Character: data category (e.g. "Carcinoma 2016")
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
 #' 
 #' @return Matrix with groups of a given dataset
 getGroupsFrom <- function(dataset, category = getCategory())
     getGlobal(category, dataset, "groups")
 
 #' Get clinical matches from a given data type
-#' @param dataset Character: data set (e.g. "Junction quantification")
-#' @param category Character: data category (e.g. "Carcinoma 2016")
 #' @note Needs to be called inside reactive function
+#' 
+#' @param dataset Character: data set (e.g. "Junction quantification")
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
 getClinicalMatchFrom <- function(dataset, category = getCategory())
     getGlobal(category, dataset, "clinicalMatch")
 
@@ -108,42 +134,68 @@ setActiveDataset <- function(dataset) setGlobal("activeDataset", value=dataset)
 
 #' Set inclusion levels for a given data category
 #' @note Needs to be called inside reactive function
+#' 
 #' @param value Data frame or matrix: inclusion levels
-#' @param category Character: data category (e.g. "Carcinoma 2016")
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
 setInclusionLevels <- function(value, category = getCategory())
     sharedData$data[[category]][["Inclusion levels"]] <- value
 
 #' Set groups from a given data type
+#' @note Needs to be called inside reactive function
+#' 
 #' @param dataset Character: data set (e.g. "Clinical data")
 #' @param groups Matrix: groups of dataset
-#' @param category Character: data category (e.g. "Carcinoma 2016")
-#' @note Needs to be called inside reactive function
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
 setGroupsFrom <- function(dataset, groups, category = getCategory())
     setGlobal(category, dataset, "groups", value=groups)
 
-#' Set table of differential analyses
-#' @param table Character: differential analyses table
-#' @param category Character: data category (e.g. "Carcinoma 2016")
+#' Set the table of differential analyses of a data category
 #' @note Needs to be called inside reactive function
+#' 
+#' @param table Character: differential analyses table
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
 setDifferentialAnalyses <- function(table, category = getCategory())
     setGlobal(category, "differentialAnalyses", value=table)
 
+#' Set the species of a data category
+#' @note Needs to be called inside reactive function
+#' 
+#' @param value Character: species
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
+setSpecies <- function(value, category = getCategory())
+    setGlobal(category, "species", value=value)
+
+#' Set the assembly version of a data category
+#' @note Needs to be called inside reactive function
+#' 
+#' @param value Character: assembly version
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
+setAssemblyVersion <- function(value, category = getCategory())
+    setGlobal(category, "assemblyVersion", value=value)
+
 #' Set clinical matches from a given data type
 #' @note Needs to be called inside reactive function
+#' 
 #' @param dataset Character: data set (e.g. "Clinical data")
 #' @param matches Vector of integers: clinical matches of dataset
-#' @param category Character: data category (e.g. "Carcinoma 2016")
+#' @param category Character: data category (e.g. "Carcinoma 2016"); by default,
+#' it uses the selected data category
 setClinicalMatchFrom <- function(dataset, matches, category = getCategory())
     setGlobal(category, dataset, "clinicalMatch", value=matches)
 
 #' Create an identifier for a given object
 #' 
-#' @param ... Arguments to identify an object
-#' 
-#' @details To make an object's identifier unique, use the names of the module,
+#' To make an object's identifier unique, use the names of the module,
 #' submodule, subsubmodule, ... as arguments before passing the name. Check the
 #' example.
 #' 
+#' @param ... Arguments to identify an object
+#' 
 #' @return Character with underscores instead of spaces
 #' 
 #' @examples

R/data_3_inclusionLevels.R

@@ -53,7 +53,11 @@ inclusionLevelsServer <- function(input, output, session) {
         startProgress("Reading alternative splicing annotation", divisions = 3)
         annot <- readRDS(system.file("extdata", input$annotation,
                                      package = "psichomics"))
-
+
+        # Set species and assembly version
+        if (grepl("Human", "Human (hg19/GRCh37)")) setSpecies("Human")
+        if (grepl("hg19", "Human (hg19/GRCh37)")) setAssemblyVersion("hg19")
+
         # Calculate inclusion levels with annotation and junction quantification
         updateProgress("Calculating inclusion levels")
         junctionQuant <- getJunctionQuantification()

R/plots_information.R

@@ -61,8 +61,11 @@ infoServer <- function(input, output, session) {
         eventPosition <- event[4:(length(event)-1)]
         eventPosition <- range(as.numeric(eventPosition))
 
-        path <- paste0("lookup/symbol/human/", gene)
-        info <- queryEnsembl(path, list(expand=1))
+        species <- tolower(getSpecies())
+        assembly <- getAssemblyVersion()
+        path <- paste0("lookup/symbol/", species, "/", gene)
+        grch37 <- assembly == "hg19"
+        info <- queryEnsembl(path, list(expand=1), grch37=grch37)
 
         output$transcripts <- renderPlot({
             transcripts <- data.frame()
@@ -99,7 +102,8 @@ infoServer <- function(input, output, session) {
 
             tagList(
                 h2(info$display_name, tags$small(info$id)),
-                sprintf("Chromosome %s: %s-%s (%s strand)",
+                sprintf("Species: %s (assembly %s)", species, assembly),
+                br(), sprintf("Chromosome %s: %s-%s (%s strand)",
                         info$seq_region_name, 
                         format(start, big.mark=",", scientific=FALSE),
                         format(end, big.mark=",", scientific=FALSE),
@@ -108,7 +112,7 @@ infoServer <- function(input, output, session) {
                               info$biotype), br(),
                 tags$a("Ensembl", icon("external-link"), target="_blank",
                        class="btn btn-link",
-                       href=paste0("http://grch37.ensembl.org/human/",
+                       href=paste0("http://grch37.ensembl.org/", species, "/",
                                    "Gene/Summary?g=", info$id)),
                 tags$a("UCSC", icon("external-link"), target="_blank",
                        class="btn btn-link",