added tax data; added midpoint color

.gitignore

@@ -1,8 +1,8 @@
 inst/doc
-inst/PhyloProfile/data/rankList.txt
-inst/PhyloProfile/data/idList.txt
-inst/PhyloProfile/data/taxonomyMatrix.txt
-inst/PhyloProfile/data/taxonNamesReduced.txt
+#inst/PhyloProfile/data/rankList.txt
+#inst/PhyloProfile/data/idList.txt
+#inst/PhyloProfile/data/taxonomyMatrix.txt
+#inst/PhyloProfile/data/taxonNamesReduced.txt
 inst/PhyloProfile/data/taxonNamesFull.txt
 inst/PhyloProfile/data/preProcessedTaxonomy.txt
 inst/PhyloProfile/data/newTaxa.txt

DESCRIPTION

@@ -11,15 +11,15 @@ Description: PhyloProfile is a tool for exploring complex phylogenetic profiles.
 URL: https://github.com/BIONF/PhyloProfileRibi/
 BugReports: https://github.com/BIONF/PhyloProfileRibi/issues
 License: MIT + file LICENSE
-Depends: R (>= 4.0.0)
+Depends: R (>= 4.1.0)
 Encoding: UTF-8
 biocViews: Software, Visualization, DataRepresentation, MultipleComparison, FunctionalPrediction
 Imports:
     BiocStyle, colourpicker, data.table, DT, energy, ggplot2, shinyBS,
     shinyjs, PhyloProfile (>= 1.6.4)
 RoxygenNote: 7.1.1
-Suggests: 
+Suggests:
     knitr, rmarkdown, testthat,
-    ape, bioDist, Biostrings, data.table, 
+    ape, bioDist, Biostrings, data.table,
     gridExtra, pbapply, RColorBrewer, shiny, OmaDB, plyr, xml2, zoo
 VignetteBuilder: knitr

R/createProfilePlot.R

@@ -6,15 +6,17 @@
 #' full or subset profiles)
 #' @param plotParameter plot parameters, including (1) type of x-axis "taxa" or
 #' "genes" - default = "taxa"; (2+3) names of 2 variables var1ID and var2ID -
-#' default = "var1" & "var2"; (4) color for lowest var1 - default = "#FF8C00";
-#' (5) color for highest var1 - default = "#4682B4"; (6) color for lowest var2 -
-#' default = "#FFFFFF", (7) color for highest var2 - default = "#F0E68C", (8)
-#' color of co-orthologs - default = "#07D000"; (9+10+11) text sizes for x, y
-#' axis and legend - default = 9 for each; (12) legend position "top", "bottom",
-#' "right", "left" or "none" - default = "top"; (13) zoom ratio of the
-#' co-ortholog dots from -1 to 3 - default = 0; (14) angle of x-axis from 0 to
-#' 90 - default = 60; (14) show/hide separate line for reference taxon 1/0 -
-#' default = 0; (15) enable/disable coloring gene categories TRUE/FALSE -
+#' default = "var1" & "var2"; (4+5) mid value and color for mid value of var1 -
+#' default is 0.5 and #FFFFFF; (6) color for lowest var1 - default = "#FF8C00";
+#' (7) color for highest var1 - default = "#4682B4"; (8+9) mid value and color
+#' for mid value of var2 - default is 1 and #FFFFFF;(10) color for lowest var2 -
+#' default = "#FFFFFF", (11) color for highest var2 - default = "#F0E68C", (12)
+#' color of co-orthologs - default = "#07D000"; (13+14+15) text sizes for x, y
+#' axis and legend - default = 9 for each; (16) legend position "top", "bottom",
+#' "right", "left" or "none" - default = "top"; (17) zoom ratio of the
+#' co-ortholog dots from -1 to 3 - default = 0; (18) angle of x-axis from 0 to
+#' 90 - default = 60; (19) show/hide separate line for reference taxon 1/0 -
+#' default = 0; (20) enable/disable coloring gene categories TRUE/FALSE -
 #' default = FALSE). NOTE: Leave blank or NULL to use default values.
 #' @param taxonHighlight taxon of interst. Default = "none".
 #' @param rankName working taxonomy rank (needed only for highlight taxon).