Merge branch 'master' into tk_workflow

Author: grlloyd

R/classical_lsq_class.R

@@ -48,7 +48,10 @@ classical_lsq<-setClass(
             value=TRUE
         ),
 
-        params.factor_names=ents$factor_names,
+        params.factor_names=entity(name='Factor name(s)',
+            description='Name of sample meta column(s) to use',
+            type=c('character','list'),
+            value='V1'),
 
         params.alpha=ents$alpha,
 

R/confounders_clsq_class.R

@@ -285,10 +285,10 @@ setMethod(f="chart.plot",
     {
 
         A=data.frame('percent_change'=double(),'group'=character())
-        for (i in 2:length(dobj$confounding_factors)) {
+        for (i in 1:length(dobj$confounding_factors)) {
             q=data.frame('percent_change'=double(nrow(dobj$percent_change)),'group'=character(nrow(dobj$percent_change)))
-            q$percent_change=dobj$percent_change[,i]*100
-            q$group=colnames(dobj$percent_change)[i]
+            q$percent_change=dobj$percent_change[,i+1]*100
+            q$group=colnames(dobj$percent_change)[i+1]
             colnames(q)=c('percent_change','group')
             A=rbind(A,q)
         }