tidy up

McTavishLab · May 31, 2018 · 5d15da4 · 5d15da4
1 parent 5214565
commit 5d15da4
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/scripts/graphical_rep.R b/scripts/graphical_rep.R
@@ -8,10 +8,8 @@ traits <- sqData[,2]
 species<-sub("'","",sqData[,1])
 species<-sub("'","",species)
 names(traits)<-species
-fitER<-fitDiscrete(sqTree, traits,model="ER")
-
-mtree<-make.simmap(sqTree,traits,model="ER")
-mtree<-make.simmap(sqTree,traits,model = matrix(c(0, 0.00000001, 0.00000001, 0), 2))
-plot(fitER)
-sqTree.label
-sqTree
+tre2<- drop.tip(sqTree, '1_9_schweinfurtii')
+mtree<-make.simmap(tre2, traits, model = matrix(c(0, 0.00000001, 0.00000001, 0), 2))
+plot(mtree,cols,type="fan",fsize=0.7,ftype="i")
+add.simmap.legend(colors=cols,prompt=FALSE,x=0.9*par()$usr[1],
+                  y=0.8*par()$usr[3],fsize=0.8)
diff --git a/scripts/otu_tidy.py b/scripts/otu_tidy.py
@@ -46,6 +46,7 @@
     new_label = "{}_{}".format(taxname,status)
     i = 0
     while new_label in new_names:
+        i += 1
         new_label = "{}{}".format(i, new_label)
     new_names.add(new_label)
     taxon.label = new_label