Fix QuSAGE.Lineage+Epi to better handle lineage ambiguous (?) populations

r.scripts/sc_QuSAGE.Epi.R

@@ -166,7 +166,11 @@ for (i in Epi){
   merge.cluster <- c(merge.cluster,as.character(factor(qs[which.max(qs$log.fold.change),1])))
 }
 sc10x.Group@ident <- plyr::mapvalues(x=sc10x.Group@ident,from=Epi,to=merge.cluster)
+if ("?" %in% names(summary(sc10x.Group@ident))){
+sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("BE","LE","OE","St","?"))
+} else {
 sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("BE","LE","OE","St"))
+}
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="EpiPop")
 
 #generate EpiPop tSNE

r.scripts/sc_QuSAGE.Lineage.R

@@ -151,7 +151,11 @@ for (i in 1:Number.Clusters){
   } else {
     merge.cluster <- c(merge.cluster,"?")
   }}
-sc10x.Group@ident <- plyr::mapvalues(x=sc10x.Group@ident,from=1:Number.Clusters,to=merge.cluster)
+if ("?" %in% names(summary(sc10x.Group@ident))){
+sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("Epi","St","?"))
+} else {
+sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("Epi","St","?"))
+}
 sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("Epi","St"))
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="Lineage")