fix #16

Author: grlloyd

R/PCA_plotfcns.R

@@ -249,18 +249,26 @@ setMethod(f="chart_plot",
         }
 
         if (is(opt$groups,'factor') | is(opt$groups,'character')) {
-            plotClass= createClassAndColors(opt$groups)
+            plotClass= structToolbox:::createClassAndColors(opt$groups)
             opt$groups=plotClass$class
         }
 
         # build the plot
-        A <- data.frame (group=opt$groups,x=x, y=y)
+        A <- data.frame (group=opt$groups,x=x, y=y,slabels=slabels)
+        
+        out = ggplot()
+        
+        # add invisible sample points for ellipse
+        out = out+geom_point(data=A,aes_string(x='x',y='y'),alpha=0,show.legend=FALSE)
+        
 
         if (length(obj$factor_name)==2) {
-            out=ggplot (data=A, aes_(x=~x,y=~y,colour=~group,label=~slabels,shape=~shapes))
+            out=out+geom_point(data=A, aes_(x=~x,y=~y,colour=~group,shape=~shapes))
         }   else {
-            out=ggplot (data=A, aes_(x=~x,y=~y,colour=~group,label=~slabels))
+            out=out+geom_point(data=A, aes_(x=~x,y=~y,colour=~group))
         }
+        
+        
         out=out+
 
             geom_point(na.rm=TRUE) +
@@ -282,12 +290,11 @@ setMethod(f="chart_plot",
         if (is(opt$groups,'factor')) { # if a factor then plot by group using the colours from pmp package
             out=out+scale_colour_manual(values=plotClass$manual_colors,
                 name=opt$factor_name)
-        }
-        else {# assume continuous and use the default colour gradient
+        }else {# assume continuous and use the default colour gradient
             out=out+scale_colour_viridis_c(limits=quantile(opt$groups,
                 c(0.05,0.95),na.rm = TRUE),oob=squish,name=opt$factor_name)
         }
-        out=out+theme_Publication(base_size = 12)
+        out=out+structToolbox:::theme_Publication(base_size = 12)
         # add ellipse for all samples (ignoring group)
         if (obj$ellipse %in% c('all','sample')) {
             out=out+stat_ellipse(type=obj$ellipse_type,mapping=aes(x=x,y=y),
@@ -310,7 +317,8 @@ setMethod(f="chart_plot",
                 {
                     temp=subset(points,!points$in.ell)
                     temp$group=opt$groups[!points$in.ell]
-                    out=out+geom_text(data=temp,aes_(x=~x,y=~y,label=~label,colour=~group),size=obj$label_size,vjust="inward",hjust="inward")
+                    temp$label=slabels[!points$in.ell]
+                    out=out+geom_text(data=temp,aes_(x=~x,y=~y,label=~label,colour=~group),size=obj$label_size,vjust="inward",hjust="inward",show.legend=FALSE)
 
                 }
             }
@@ -319,9 +327,8 @@ setMethod(f="chart_plot",
         }
 
         # label all points if requested
-        if (opt$points_to_label=='all')
-        {
-            out=out+geom_text(vjust="inward",hjust="inward")
+        if (opt$points_to_label=='all') {
+            out=out+geom_text(data=A,aes_string(x='x',y='y',colour='group',label='slabels'),vjust="inward",hjust="inward",show.legend=FALSE)
         }
 
         return(out)