Bioc revision2 - cont. (#102)

* removed commented out codes

* resolved functions in functions for compareTaxaGroups.R

* replaced return() by stop() with error msg

* replaced return() by stop() with error msg for functions in inst/PhyloProfile/R

* version bump

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: PhyloProfile
-Version: 0.99.19
+Version: 0.99.20
 Date: 2019-08-06
 Title: PhyloProfile
 Authors@R: c(

NAMESPACE

@@ -26,6 +26,7 @@ export(featureDistTaxPlot)
 export(filterProfileData)
 export(fromInputToProfile)
 export(geneAgePlotDf)
+export(generateSinglePlot)
 export(getAllDomainsOma)
 export(getAllFastaOma)
 export(getCommonAncestor)
@@ -49,6 +50,7 @@ export(getSelectedFastaOma)
 export(getSelectedTaxonNames)
 export(getTaxonomyMatrix)
 export(getTaxonomyRanks)
+export(gridArrangeSharedLegend)
 export(heatmapPlotting)
 export(highlightProfilePlot)
 export(parseDomainInput)
@@ -68,6 +70,8 @@ import(ExperimentHub)
 import(data.table)
 import(energy)
 import(ggplot2)
+import(grid)
+import(gridExtra)
 import(shinyBS)
 import(shinycssloaders)
 import(shinyjs, except = colourInput)

R/analyzeDistribution.R

@@ -14,9 +14,10 @@
 #' createPercentageDistributionData(mainLongRaw, "class")
 
 createPercentageDistributionData <- function(inputData, rankName = NULL) {
-    if (is.null(inputData) | is.null(rankName)) return()
+    if (is.null(inputData) | is.null(rankName)) 
+        stop("Input data or rank name cannot be NULL!")
     allMainRanks <- getTaxonomyRanks()
-    if (!(rankName[1] %in% allMainRanks)) return("Invalid taxonomy rank given!")
+    if (!(rankName[1] %in% allMainRanks)) stop("Invalid taxonomy rank given!")
 
     if (ncol(inputData) < 4) {
         colnames(inputData) <- c("geneID", "ncbiID", "orthoID")
@@ -151,7 +152,8 @@ createVariableDistributionDataSubset <- function(
     supertaxonMod <- NULL
 
     # check parameters
-    if (is.null(fullProfileData) | is.null(distributionData)) return()
+    if (is.null(fullProfileData) | is.null(distributionData)) 
+        stop("Full processed profiles or distribution data cannot be NULL!")
 
     # get geneID and supertaxon name for distributionData
     distributionDataName <- merge(
@@ -235,7 +237,7 @@ createVarDistPlot <- function(
     data, varName = "var", varType = "var1", percent = c(0, 1),
     distTextSize = 12
 ) {
-    if (is.null(data)) return()
+    if (is.null(data)) stop("Input data cannot be NULL!")
     if (varType == "presSpec") {
         # remove presSpec < cutoffMin or > cutoffMax
         if (percent[1] > 0) {

R/clusterProfile.R

@@ -28,7 +28,7 @@ getDataClustering <- function(
     data = NULL, profileType = "binary",
     var1AggregateBy = "max", var2AggregateBy = "max"
 ) {
-    if (is.null(data)) return()
+    if (is.null(data)) stop("Input data cannot be NULL!")
     supertaxon <- NULL
     presSpec <- NULL
 
@@ -97,7 +97,7 @@ getDataClustering <- function(
 #' getDistanceMatrix(profiles, method)
 
 getDistanceMatrix <- function(profiles = NULL, method = "mutualInformation") {
-    if (is.null(profiles)) return()
+    if (is.null(profiles)) stop("Profile data cannot be NULL!")
     profiles <-  profiles[, colSums(profiles != 0) > 0]
     profiles <-  profiles[rowSums(profiles != 0) > 0, ]
 
@@ -157,7 +157,7 @@ getDistanceMatrix <- function(profiles = NULL, method = "mutualInformation") {
 #' clusterDataDend(distanceMatrix, clusterMethod)
 
 clusterDataDend <- function(distanceMatrix = NULL, clusterMethod = "complete") {
-    if (is.null(distanceMatrix)) return()
+    if (is.null(distanceMatrix)) stop("Distance matrix cannot be NULL!")
     dd.col <- hclust(distanceMatrix, method = clusterMethod)
     return(dd.col)
 }
@@ -181,7 +181,7 @@ clusterDataDend <- function(distanceMatrix = NULL, clusterMethod = "complete") {
 #' getDendrogram(dd)
 
 getDendrogram <- function(dd = NULL) {
-    if (is.null(dd)) return()
+    if (is.null(dd)) stop("Input dendrogram cannot be NULL!")
     p <- ape::plot.phylo(as.phylo(dd))
     return(p)
 }