@@ -202,7 +202,7 @@ setMethod(f="chart_plot",

         }

         # build the plot

-        A <- data.frame (group=groups,x=x, y=y,slabels=slabels)

+        A <- data.frame (group=groups,x=x, y=y,slabels=slabels,shape=shapes)

         out = ggplot()

@@ -210,10 +210,11 @@ setMethod(f="chart_plot",

         out = out+geom_point(data=A,aes_string(x='x',y='y'),alpha=0,show.legend=FALSE)

         if (length(shapes)>1) {

-            out=out+geom_point(data=A, aes_(x=~x,y=~y,colour=~group,shape=~shapes))

+            out=out+geom_point(data=A, aes_(x=~x,y=~y,colour=~group,shape=~shape)) 

         } else {

-            out=out+geom_point(data=A, aes_(x=~x,y=~y,colour=~group),shape=shapes)

+            out=out+geom_point(data=A, aes_(x=~x,y=~y,colour=~group),shape=shapes) 

         }

+

         out=out+

             geom_point(na.rm=TRUE) +

@@ -227,16 +228,23 @@ setMethod(f="chart_plot",

         }

         if (obj$ellipse %in% c('all','group')) {

-            out = out +stat_ellipse(data=A, aes_(x=~x,y=~y,colour=~group),type=obj$ellipse_type,

+            if (is.factor(groups)) {

+            out = out +stat_ellipse(data=A, aes_(x=~x,y=~y,colour=~group,group=~group),type=obj$ellipse_type,

                 level=obj$ellipse_confidence) # ellipse for individual groups

+            } else {

+                if (is.factor(shapes)) {

+                    out = out +stat_ellipse(data=A, aes_(x=~x,y=~y,group=~shape),color="#C0C0C0",type=obj$ellipse_type,

+                        level=obj$ellipse_confidence) # ellipse for individual groups

+                }

+            }

         }

         if (is(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=obj$factor_name[[1]])

-        }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(groups,

-                c(0.05,0.95),na.rm = TRUE),oob=squish,name=obj$factor_name[[1]])

+                c(0.05,0.95),na.rm = TRUE),oob=scales::squish,name=obj$factor_name[[1]])

         }

         out=out+theme_Publication(base_size = 12)

         # add ellipse for all samples (ignoring group)