Merge branch 'trvinh-master'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PhyloProfile
-Version: 0.99.6
-Date: 2019-04-24
+Version: 0.99.7
+Date: 2019-05-13
 Title: PhyloProfile
 Authors@R: c(
     person("Vinh", "Tran", email = "tran@bio.uni-frankfurt.de", role = c("aut", "cre")),
@@ -17,9 +17,10 @@ biocViews: Software, Visualization, DataRepresentation, MultipleComparison, Func
 Imports:
     ape, bioDist, BiocStyle, Biostrings, Cairo, colourpicker, data.table,
     dendextend, devtools, dplyr, DT, energy, IRanges, GenomeInfoDbData, ggplot2,
-    gplots, GO.db, grDevices, gridExtra, gtable, knitr, RColorBrewer, RCurl, 
-    reshape2, rmarkdown, scales, shiny, shinyBS, shinycssloaders, shinyjs, 
-    stats, stringr, svMisc, tidyr, utils, OmaDB, plyr, xml2, zoo
+    gplots, GO.db, grDevices, grid, gridExtra, gtable, knitr, pbapply,
+    RColorBrewer, RCurl, reshape2, rmarkdown, scales, shiny, shinyBS, 
+    shinycssloaders, shinyjs, stats, stringr, svMisc, tidyr, utils, OmaDB, plyr,
+    xml2, zoo
 RoxygenNote: 6.1.1
 Suggests:
     testthat

NAMESPACE

@@ -5,20 +5,25 @@ export(checkInputValidity)
 export(checkNewick)
 export(checkOmaID)
 export(clusterDataDend)
+export(compareMedianTaxonGroups)
+export(compareTaxonGroups)
 export(createArchiPlot)
 export(createGeneAgePlot)
 export(createLongMatrix)
 export(createPercentageDistributionData)
-export(createProfileData)
 export(createProfileFromOma)
 export(createRootedTree)
 export(createVarDistPlot)
 export(createVariableDistributionData)
 export(createVariableDistributionDataSubset)
 export(dataCustomizedPlot)
+export(dataFeatureTaxGroup)
 export(dataMainPlot)
+export(dataVarDistTaxGroup)
 export(estimateGeneAge)
 export(fastaParser)
+export(featureDistTaxPlot)
+export(filterProfileData)
 export(fromInputToProfile)
 export(geneAgePlotDf)
 export(getAllDomainsOma)
@@ -29,7 +34,10 @@ export(getDataClustering)
 export(getDataForOneOma)
 export(getDendrogram)
 export(getDistanceMatrix)
-export(getFastaSeqs)
+export(getFastaDemo)
+export(getFastaFromFasInput)
+export(getFastaFromFile)
+export(getFastaFromFolder)
 export(getIDsRank)
 export(getInputTaxaID)
 export(getInputTaxaName)
@@ -39,7 +47,7 @@ export(getOmaDomainFromURL)
 export(getOmaMembers)
 export(getQualColForVector)
 export(getSelectedFastaOma)
-export(getSignificantGenes)
+export(getSelectedTaxonNames)
 export(getTaxonomyMatrix)
 export(getTaxonomyRanks)
 export(heatmapPlotting)
@@ -51,6 +59,8 @@ export(runPhyloProfile)
 export(sortInputTaxa)
 export(sortTaxaFromTree)
 export(taxonomyTableCreator)
+export(varDistTaxPlot)
+export(wideToLong)
 export(xmlParser)
 import(BiocStyle)
 import(Cairo)
@@ -71,6 +81,7 @@ import(scales)
 import(shinyBS)
 import(shinycssloaders)
 import(shinyjs, except = colourInput)
+import(svMisc)
 import(tidyr)
 importFrom(Biostrings,readAAStringSet)
 importFrom(IRanges,reverse)
@@ -86,29 +97,40 @@ importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_boxplot)
 importFrom(ggplot2,geom_histogram)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_rect)
 importFrom(ggplot2,geom_segment)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,geom_violin)
 importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggplotGrob)
 importFrom(ggplot2,guide_colourbar)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
+importFrom(ggplot2,position_dodge)
 importFrom(ggplot2,scale_color_gradient)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_fill_brewer)
 importFrom(ggplot2,scale_fill_gradient)
 importFrom(ggplot2,scale_size_continuous)
+importFrom(ggplot2,scale_x_discrete)
 importFrom(ggplot2,scale_y_discrete)
 importFrom(ggplot2,scale_y_reverse)
+importFrom(ggplot2,stat_summary)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
+importFrom(ggplot2,theme_void)
 importFrom(grDevices,colorRampPalette)
+importFrom(grid,gpar)
+importFrom(grid,textGrob)
+importFrom(grid,unit)
+importFrom(grid,unit.c)
 importFrom(gridExtra,arrangeGrob)
 importFrom(plyr,mapvalues)
 importFrom(reshape2,melt)
@@ -118,8 +140,8 @@ importFrom(stats,as.dist)
 importFrom(stats,complete.cases)
 importFrom(stats,hclust)
 importFrom(stats,ks.test)
+importFrom(stats,median)
 importFrom(stats,na.omit)
-importFrom(stats,p.adjust)
 importFrom(stats,wilcox.test)
 importFrom(stringr,regex)
 importFrom(stringr,str_count)