Merge pull request #326 from mixOmicsTeam/issue-307

PR addressing Issue #307

R/internal_graphicModule.R

@@ -117,7 +117,9 @@ internal_graphicModule <-
                 group.pch = "different"
         }
 
-        df$pch.levels = factor(as.character(df$pch.levels)) #forced to be character,
+        # removed code to force as.character below because pch.levels should never be reordered, always the same (1, 2, 3, 4..) and they should always match the order of df$group levels
+        df$pch.levels = factor(as.numeric(df$pch.levels))
+        #df$pch.levels = factor(as.character(df$pch.levels)) #forced to be character,
         #   so that the order of the levels is the same all the time
         #   (1, 10, 11, 12, 2, 3...), instead of changing between ggplot2 and
         #   the rest
@@ -218,25 +220,22 @@ internal_graphicModule <-
 
 
             #-- Modify scale colour - Change X/Ylabel - split plots into Blocks
-            p = p + scale_color_manual(values = unique(col.per.group)[match(
-                levels(factor(as.character(df$group))), levels(df$group))],
-                name = legend.title)
+            ## order of 'col.per.group' will correspond to order of levels in 'df$group'
+            p = p + scale_color_manual(values = col.per.group, name = legend.title)
 
 
             if(group.pch == "same")
             {
-                p = p + scale_shape_manual(values = values.pch[match(
-                    levels(factor(as.character(df$pch.levels))),levels(df$pch.levels))],
+                p = p + scale_shape_manual(values = values.pch,
                     name = legend.title, labels = levels(factor(df$group)),
                     guide = "none")
                 #match(..) reorder the values as the values of pch.levels,
                 #if there's more than 10 levels, R/ggplot orders characters
                 #different than values 1, 10, 11, 2, 3, etc
             } else {
                 # if pch different factor, then second legend
-                p = p + scale_shape_manual(values = values.pch[match(
-                    levels(factor(as.character(df$pch.levels))),levels(df$pch.levels))],
-                    name = legend.title.pch, labels = levels(df$pch.levels))
+                p = p + scale_shape_manual(values = values.pch,
+                    name = legend.title.pch, labels = values.pch)
             }
 
             p = p + #labs(list(title = title, x = X.label, y = Y.label)) +
@@ -294,12 +293,13 @@ internal_graphicModule <-
                 if (display.names | any(class.object%in%object.mint) ) {
                     group.shape <- 19
                 } else {
-                    group.shape <- unique(df$pch.legend)
+                    # keep order of pch.levels the same
+                    group.shape <- as.numeric(levels(df$pch.levels))
 
                     if (length(group.shape) > 1)
                     {
-                        names(group.shape) <- unique(df$group)
-                        group.shape <- group.shape[sort(names(group.shape))]
+                        # keep order of df$group levels the same
+                        names(group.shape) <- levels(df$pch.legend)
                     }
                 }
 
@@ -398,8 +398,7 @@ internal_graphicModule <-
             }
 
             #-- Modify scale colour - Change X/Ylabel - split plots into Blocks
-            p = p + scale_colour_manual(values = unique(col.per.group)[match(
-                levels(factor(as.character(df$group))), levels(df$group))],
+            p = p + scale_colour_manual(values = unique(col.per.group),
                 name = legend.title) +
                 labs(shape = "Study")#levels(object$study)[study.ind])
 
@@ -812,9 +811,11 @@ internal_graphicModule <-
                              lwd=point.lwd)#,...)
                     } else {
                         points(x = df[df$col == i & other, "x"],
-                               y = df[df$col == i & other, "y"],
-                               col = df[df$col == i, ]$col, cex = df[df$col == i, ]$cex,
-                               pch = df[df$col == i, ]$pch,lwd=point.lwd)#,...)
+                        y = df[df$col == i & other, "y"],
+                        col = df[df$col == i, ]$col, 
+                        cex = df[df$col == i, ]$cex,
+                        pch = as.numeric(df[df$col == i, ]$pch.levels),
+                        lwd=point.lwd)#,...)
                     }
                 }
 

R/plotIndiv.R

@@ -69,7 +69,8 @@
 #' @param group factor indicating the group membership for each sample, useful
 #' for ellipse plots. Coded as default for the supervised methods \code{PLS-DA,
 #' SPLS-DA,sGCCDA}, but needs to be input for the unsupervised methods
-#' \code{PCA, sPCA, IPCA, sIPCA, PLS, sPLS, rCC, rGCCA, sGCCA}
+#' \code{PCA, sPCA, IPCA, sIPCA, PLS, sPLS, rCC, rGCCA, sGCCA}. Order of levels will reflect
+#' order in legends and correspond to any set colours. 
 #' @template arg/col.per.group
 #' @param style argument to be set to either \code{'graphics'},
 #' \code{'lattice'}, \code{'ggplot2'} or \code{'3d'} for a style of plotting.