renamed to PhyloRBF

BIONF · Jul 9, 2021 · a0ba47c · a0ba47c
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -29,5 +29,3 @@ Don't hesitate to get in touch with us if you have any questions. You can contac
 
 ### Contributors
 * [Vinh Tran](https://github.com/trvinh)
-* [Bastian Greshake Tzovaras](https://github.com/gedankenstuecke)
-* [Carla Moelbert](https://github.com/CarlaMoelbert)
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
-Package: PhyloProfileRibi
+Package: PhyloRBF
 Version: 1.0.0
-Date: 2021-06-22
-Title: PhyloProfileRibi
+Date: 2021-07-09
+Title: PhyloRBF
 Authors@R: c(
     person("Vinh", "Tran", role = c("aut", "cre"), email = "[email protected]"),
     person("Bastian", "Greshake Tzovaras", role = "aut", email = "[email protected]"),
     person("Ingo", "Ebersberger", role = "aut", email = "[email protected]"),
     person("Carla", "Mölbert", role = "ctb", email = "[email protected]"))
 Description: PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.
-URL: https://github.com/BIONF/PhyloProfileRibi/
-BugReports: https://github.com/BIONF/PhyloProfileRibi/issues
+URL: https://github.com/BIONF/PhyloRBF/
+BugReports: https://github.com/BIONF/PhyloRBF/issues
 License: MIT + file LICENSE
 Depends: R (>= 4.1.0)
 Encoding: UTF-8

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2016 Vinh Tran
+Copyright (c) 2021 Vinh Tran
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/NAMESPACE b/NAMESPACE
@@ -5,7 +5,7 @@ export(getNameListCr)
 export(getSelectedTaxonNamesCr)
 export(getTaxonomyMatrixCr)
 export(highlightProfilePlotCr)
-export(runPhyloProfileRibi)
+export(runPhyloRBF)
 export(sortInputTaxaCr)
 import(BiocStyle)
 import(DT)

diff --git a/R/createProfilePlot.R b/R/createProfilePlot.R
@@ -38,7 +38,7 @@ highlightProfilePlotCr <- function(
     if (taxonHighlight != "none") {
         # get selected highlight taxon ID
         nameReducedFile <- paste(
-            system.file(package = "PhyloProfileRibi"),
+            system.file(package = "PhyloRBF"),
             "PhyloProfile/data/taxonNamesReduced.txt", sep="/")
         if (!file.exists(nameReducedFile)) {
             taxonNamesReduced <- NULL

diff --git a/R/parsePhyloProfile.R b/R/parsePhyloProfile.R
@@ -8,7 +8,7 @@
 
 getNameListCr <- function() {
     nameReducedFile <- paste(
-        system.file(package="PhyloProfileRibi"),
+        system.file(package="PhyloRBF"),
         "PhyloProfile/data/taxonNamesReduced.txt",
         sep="/"
     )
@@ -41,7 +41,7 @@ getNameListCr <- function() {
 
 getTaxonomyMatrixCr <- function(subsetTaxaCheck = FALSE, taxonIDs = NULL){
     taxonomyMatrixFile <- paste(
-        system.file(package="PhyloProfileRibi"),
+        system.file(package="PhyloRBF"),
         "PhyloProfile/data/taxonomyMatrix.txt",
         sep="/"
     )

diff --git a/R/runPhyloprofile.R b/R/runPhyloprofile.R
@@ -9,11 +9,11 @@
 #' @rawNamespace import(RCurl, except = reset)
 #' @rawNamespace import(shinyjs, except = colourInput)
 
-runPhyloProfileRibi <- function(){
-    appDir <- system.file("PhyloProfile", package = "PhyloProfileRibi")
+runPhyloRBF <- function(){
+    appDir <- system.file("PhyloProfile", package = "PhyloRBF")
     if (appDir == "") {
         stop(
-            "Could not find apps directory. Try re-installing `PhyloProfileRibi`.",
+            "Could not find apps directory. Try re-installing `PhyloRBF`.",
             call = FALSE
         )
     }

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-# PhyloProfileRibi
+# PhyloRBF
 
-The data of PhyloProfile Ribosome Biogenesis is displayed for an interactive exploration of the [feature-aware phylogenetic profile of ???](https://applbio.biologie.uni-frankfurt.de/phyloprofileribi/).
+The data of PhyloProfile Ribosome Biogenesis is displayed for an interactive exploration of the [feature-aware phylogenetic profile of ???](https://applbio.biologie.uni-frankfurt.de/PhyloRBF/).
 This is a lite version of [PhyloProfile](https://github.com/BIONF/PhyloProfile), which is pre-configured only for its use with the [Ribosome biogenesis data](https://applbio.biologie.uni-frankfurt.de/download/RibosomeBiogenesis/).
 
 # Table of Contents
@@ -21,10 +21,10 @@ Feature-aware phylogenetic profile of the yeast ribosome biogenesis genes across
 * For further details on the biological interpretation of the data, please refer to the article [DO WE HAVE A LINK SOMEWHERE](https://www.biorxiv.org/content/10.1101/2021.01.29.428808v2).
 
 # Bugs
-Any bug reports or comments, suggestions are highly appreciated. Please [open an issue on GitHub](https://github.com/BIONF/PhyloProfileRibi/issues/new) or be in touch via email.
+Any bug reports or comments, suggestions are highly appreciated. Please [open an issue on GitHub](https://github.com/BIONF/PhyloRBF/issues/new) or be in touch via email.
 
 # License
-This tool is released under [MIT license](https://github.com/BIONF/PhyloProfileRibi/blob/master/LICENSE).
+This tool is released under [MIT license](https://github.com/BIONF/PhyloRBF/blob/master/LICENSE).
 
 # Contact
 Ingo Ebersberger

diff --git a/inst/PhyloProfile/R/createProfilePlot.R b/inst/PhyloProfile/R/createProfilePlot.R
@@ -67,7 +67,7 @@ createProfilePlot <- function(input, output, session,
             if (inSeq()[1] == "all" & inTaxa()[1] == "all") return()
         }
         withProgress(message = 'PLOTTING...', value = 0.5, {
-            PhyloProfileRibi::highlightProfilePlotCr(
+            PhyloRBF::highlightProfilePlotCr(
                 dataHeat(),
                 parameters(),
                 taxonHighlight(),
@@ -103,7 +103,7 @@ createProfilePlot <- function(input, output, session,
         content = function(file) {
             ggsave(
                 file,
-                plot = PhyloProfileRibi::highlightProfilePlotCr(
+                plot = PhyloRBF::highlightProfilePlotCr(
                     dataHeat(), parameters(), "none", rankSelect(), "none"
                 ),
 
@@ -116,7 +116,7 @@ createProfilePlot <- function(input, output, session,
     # get info of clicked point on heatmap plot --------------------------------
     selectedpointInfo <- reactive({
         # get selected supertaxon name
-        taxaList <- PhyloProfileRibi::getNameListCr()
+        taxaList <- PhyloRBF::getNameListCr()
         rankName <- rankSelect()
         inSelect <- taxaList$ncbiID[taxaList$fullName == inSelect()]
 

diff --git a/inst/PhyloProfile/server.R b/inst/PhyloProfile/server.R
@@ -227,7 +227,7 @@ shinyServer(function(input, output, session) {
         withProgress(message = 'Reading main input...', value = 0.5, {
             # inFile <- system.file(
             #     "extdata", "ribi/ribi.phyloprofile",
-            #     package="PhyloProfileRibi"
+            #     package="PhyloRBF"
             # )
             inFile <- "data/ribi.phyloprofile"
             longDataframe <- createLongMatrix(inFile)
@@ -265,7 +265,7 @@ shinyServer(function(input, output, session) {
             domainFile <- "data/ribi.domains"
             # domainFile <- system.file(
             #     "extdata", "ribi/ribi.domains",
-            #     package="PhyloProfileRibi"
+            #     package="PhyloRBF"
             # )
             domainDf <- parseDomainInput(NULL, domainFile, "file")
             return(domainDf)
@@ -286,7 +286,7 @@ shinyServer(function(input, output, session) {
         req(getMainInput())
         if (input$rankSelect == "") return()
         withProgress(message = 'Getting input taxon names...', value = 0.5, {
-            inputTaxaName <- PhyloProfileRibi::getInputTaxaNameCr(
+            inputTaxaName <- PhyloRBF::getInputTaxaNameCr(
               input$rankSelect, inputTaxonID()
             )
             return(inputTaxaName)
@@ -299,12 +299,12 @@ shinyServer(function(input, output, session) {
             # get input taxonomy tree
             # treeIn <- system.file(
             #     "extdata", "ribi/ribi.nwk",
-            #     package="PhyloProfileRibi"
+            #     package="PhyloRBF"
             # )
             # inputTaxaTree <- read.tree(file = treeIn)
 
             # sort taxonomy matrix based on selected refTaxon
-            sortedOut <- PhyloProfileRibi::sortInputTaxaCr(
+            sortedOut <- PhyloRBF::sortInputTaxaCr(
                 taxonIDs = inputTaxonID(),
                 rankName = input$rankSelect,
                 refTaxon = getRefspec(input$rankSelect),
@@ -1045,7 +1045,7 @@ shinyServer(function(input, output, session) {
         fastain <- "data/ribi.fasta"
         # fastain <- system.file(
         #     "extdata", "ribi/ribi.fasta",
-        #     package="PhyloProfileRibi"
+        #     package="PhyloRBF"
         # )
         fastaOut <- getFastaFromFile(seqID, fastain)
         return(paste(fastaOut[1]))
@@ -1074,7 +1074,7 @@ shinyServer(function(input, output, session) {
         fastain <- "data/ribi.fasta"
         # fastain <- system.file(
         #     "extdata", "ribi/ribi.fasta",
-        #     package="PhyloProfileRibi"
+        #     package="PhyloRBF"
         # )
         mainFastaOut <- getFastaFromFile(seqIDs, fastain)
         return(mainFastaOut)
@@ -1100,7 +1100,7 @@ shinyServer(function(input, output, session) {
         fastain <- "data/ribi.fasta"
         # fastain <- system.file(
         #     "extdata", "ribi/ribi.fasta",
-        #     package="PhyloProfileRibi"
+        #     package="PhyloRBF"
         # )
         fastaOutDf <- getFastaFromFile(seqIDs, fastain)
         return(fastaOutDf)

diff --git a/inst/PhyloProfile/ui.R b/inst/PhyloProfile/ui.R
@@ -10,7 +10,7 @@ shinyUI(
         useShinyjs(),
 
         # Application title
-        titlePanel("", windowTitle = "PhyloProfileRibi"),
+        titlePanel("", windowTitle = "PhyloRBF"),
 
         # TOP WELLPANEL FOR PLOT CONFIGURATION ---------------------------------
         conditionalPanel(
@@ -149,7 +149,7 @@ shinyUI(
 
         # MAIN NARVARPAGE TABS -------------------------------------------------
         navbarPage(
-            em(strong("PhyloProfile Ribosome Biogenesis")),
+            em(strong("PhyloRBF")),
             id = "tabs",
             collapsible = TRUE,
             inverse = TRUE,
@@ -326,7 +326,7 @@ shinyUI(
                 tabPanel(
                     a(
                         "About",
-                        href = "https://BIONF.github.io/PhyloProfileRibi/",
+                        href = "https://BIONF.github.io/PhyloRBF/",
                         target = "_blank"
                     )
                 )

diff --git a/man/highlightProfilePlotCr.Rd b/man/highlightProfilePlotCr.Rd
diff --git a/man/runPhyloProfileRibi.Rd → man/runPhyloRBF.Rd b/man/runPhyloProfileRibi.Rd → man/runPhyloRBF.Rd