vegan_wrapper 2 category doesn't do polygon

jtclaypool · May 9, 2017 · d24e436 · d24e436
1 parent 7e33109
commit d24e436
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/R/vegan_wrapper.R b/R/vegan_wrapper.R
@@ -29,10 +29,9 @@ vegan_wrapper <- function(RA="relative abundance",meta="metadata",category_1="ca
   if(labels){nmds_dat=nmds_dat[match(meta[,1],rownames(nmds_dat)),]}
 
   if(!is.na(category_2)){
-    nmds_dat=cbind.data.frame(nmds_dat,"combined"=paste(meta[,category_1],meta[,category_2],sep="_"))
+    nmds_dat=cbind.data.frame(nmds_dat,"category_1"=meta[,category_1],"category_2"=meta[,category_2])
     NMDS_plot <- ggplot(data = nmds_dat,aes(x=MDS1,y=MDS2))+
-    geom_polygon(data=nmds_dat,aes(fill=as.factor(combined)))+
-    geom_point(aes(fill=as.factor(combined)))
+    geom_point(aes(shape=as.factor(category_2),color=(as.factor(category_1))))
   }
   else{
     NMDS_plot <- ggplot(data = nmds_dat,aes(x=MDS1,y=MDS2))+