fixed order detailed plot; mVar for co-orthologs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PhyloProfile
-Version: 1.17.0
-Date: 2023-09-12
+Version: 1.17.1
+Date: 2024-02-01
 Title: PhyloProfile
 Authors@R: c(
     person("Vinh", "Tran", role = c("aut", "cre"), email = "[email protected]", comment=c(ORCID="0000-0001-6772-7595")),

R/parsePhyloProfile.R

@@ -707,11 +707,14 @@ reduceProfile <- function(filteredProfile) {
     if (length(unique(levels(as.factor(filteredProfile$numberSpec)))) == 1) {
         if (unique(levels(as.factor(filteredProfile$numberSpec))) == 1) {
             superDfExt <- filteredProfile[, c(
-                "geneID", "supertaxon", "supertaxonID",
-                "var1", "presSpec", "category", "orthoID", "var2", "paralog"
+                "geneID", "supertaxon", "supertaxonID", "orthoID", "category", 
+                "presSpec", "paralog", "mVar1", "mVar2"
             )]
             superDfExt$presentTaxa <- 1
             superDfExt$totalTaxa <- 1
+            # rename mVar to var
+            names(superDfExt)[names(superDfExt) == "mVar1"] <- "var1"
+            names(superDfExt)[names(superDfExt) == "mVar2"] <- "var2"
             flag <- 0
         }
     }

inst/PhyloProfile/R/createDetailedPlot.R

@@ -148,6 +148,11 @@ createDetailedPlot <- function(
     return(pointInfoDetail)
 }
 
+prepareDf <- function(selDf) {
+    selDf <- selDf[with(dataframe, order(fullName, orthoID)),]
+    selDf$xLabel <- paste(selDf$orthoID, " (", selDf$fullName, ")", sep = "")
+    return(selDf)
+}
 
 #' create detailed plot
 #' @param selDf data for plotting  (from reactive fn "detailPlotDt")
@@ -177,7 +182,7 @@ detailPlot <- function(selDf, detailedText, var1ID, var2ID){
     }
 
     # keep order of ID (xLabel)
-    # detailedDf$id <- factor(detailedDf$id, levels = unique(detailedDf$id))
+    detailedDf$id <- factor(detailedDf$id, levels = unique(detailedDf$id))
 
     # create plot
     gp <- ggplot(detailedDf, aes(y = score, x = id, fill = var)) +