Fixed a bug in heatMapPAM

wanyuac · Aug 8, 2022 · e808430 · e808430
1 parent 07c13cb
commit e808430
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Showing 36 changed files with 438 additions and 141 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: GeneMates
 Type: Package
 Title: Analysing association and physical linkage between bacterial genes
-Version: 0.2.2
+Version: 0.2.3
 Author: Yu Wan
 Maintainer: Yu Wan <[email protected]>
 Description: Applies univariate linear mixed models (LMMs) to bacterial genotype
@@ -24,4 +24,4 @@ Imports:
     networkDynamic (>= 0.9.0),
     vegan (>= 2.4-4),
     reshape2 (>= 1.4)
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.0
diff --git a/R/func__visualisation__heatMapPAM.R b/R/func__visualisation__heatMapPAM.R
@@ -53,7 +53,7 @@
 #' @export
 #' @author Guangchuang Yu, Yu Wan (\email{wanyuac@@126.com})
 #
-# First edition of this function: 5 Sep 2018; the latest edition: 28 Aug 2019
+# First edition of this function: 5 Sep 2018; the latest edition: 8 Aug 2022
 # Licence: Artistic License 2.0 (follow the licence of the package ggtree)
 
 heatMapPAM <- function(p, data, col_colours = "black", null_colour = "grey90",
@@ -213,10 +213,11 @@ heatMapPAM <- function(p, data, col_colours = "black", null_colour = "grey90",
         # scale_fill_manual sets tile colours; scale_colour_manual sets label colours
         p2 <- p2 + scale_fill_manual(name = "Class",
                                      breaks = c("0", as.character(colour_codes)),
-                                     values = colours_uniq, na.value = NA) +
-            scale_colour_manual(name = "Class",
-                                breaks = c("0", as.character(colour_codes)),
-                                values = colours_uniq, na.value = NA)
+                                     values = colours_uniq, na.value = NA)
+            # Bug identified (8/8/2022): loss of tip labels after scalling colours
+            # + scale_colour_manual(name = "Class",
+            #                    breaks = c("0", as.character(colour_codes)),
+            #                    values = colours_uniq, na.value = NA)
     } else {
         p2 <- p2 + scale_fill_manual(name = "Class", breaks = c("1", "0"),
                                values = c("1" = col_colours, "0" = null_colour),

diff --git a/man/allelicCoMatrix.Rd b/man/allelicCoMatrix.Rd
diff --git a/man/betaSignCongruence.Rd b/man/betaSignCongruence.Rd
diff --git a/man/calcAllelicDiveristyPerCountry.Rd b/man/calcAllelicDiveristyPerCountry.Rd
diff --git a/man/comparePvalues.Rd b/man/comparePvalues.Rd
diff --git a/man/corCladeProj.Rd b/man/corCladeProj.Rd
diff --git a/man/countAllelesPerCountry.Rd b/man/countAllelesPerCountry.Rd
diff --git a/man/countAllelesPerYear.Rd b/man/countAllelesPerYear.Rd
diff --git a/man/drawHeatMap.Rd b/man/drawHeatMap.Rd
diff --git a/man/evalPL.Rd b/man/evalPL.Rd
diff --git a/man/findMinIncClade.Rd b/man/findMinIncClade.Rd
diff --git a/man/findMinIncCladeOfStrains.Rd b/man/findMinIncCladeOfStrains.Rd
diff --git a/man/findPhysLink.Rd b/man/findPhysLink.Rd
diff --git a/man/findSeq.Rd b/man/findSeq.Rd
diff --git a/man/getClusterMemberCooccurrence.Rd b/man/getClusterMemberCooccurrence.Rd
diff --git a/man/heatMapPAM.Rd b/man/heatMapPAM.Rd