phylofactorization updates

reptalex · Jul 7, 2018 · 3ab245e · 3ab245e
1 parent aef707a
commit 3ab245e
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Showing 2 changed files with 6 additions and 8 deletions.
diff --git a/R/PhyloFactor.R b/R/PhyloFactor.R
@@ -339,7 +339,7 @@ PhyloFactor <- function(Data,tree,X=NULL,frmla = Data~X,choice='var',transform.f
     }
     tree <- ape::drop.tip(tree,setdiff(tree$tip.label,rownames(Data)))}
   if (!all(rownames(Data)==tree$tip.label)){
-    warning('rows of data are in different order of tree tip-labels - use output$data for downstream analysis, or set Data <- Data[tree$tip.label,]')
+    warning('rows of data are in different order of tree tip-labels - use output$data for downstream analysis, or set Data <- Data[output$tree$tip.label,]')
     Data <- Data[tree$tip.label,]
   }
 

diff --git a/R/pf.heatmap.R b/R/pf.heatmap.R
@@ -58,18 +58,16 @@ pf.heatmap <- function(PF=NULL,tree=NULL,Data=NULL,factors=NULL,column.order=NUL
 
   if (!is.null(Data)){
     if (nrow(Data) != length(PF$tree$tip.label)){
-      stop('number of rows of Data does not equal number of columns in PF$tree tip-labels')
+      stop('number of rows of Data does not equal number of tips in PF$tree')
     } else {
       if (is.null(rownames(Data))){
+        warning('No rownames of input Data - pf.heatmap will assume rows are in same order of tree tip labels')
         rownames(Data) <- PF$tree$tip.label
       } else {
-        if (!all.equal(rownames(Data),PF$tree$tip.label)){
-          if (!all.equal(sort(rownames(Data)),sort(PF$tree$tip.label))){
-            warning('Rownames of Data cannot be matched with PF$tree tip-labels. Assuming rows are in same order as tree tip-labels')
-            rownames(Data) <- PF$tree$tip.label
-          } else {
+        if (!all(rownames(Data) %in% PF$tree$tip.label & all(PF$tree$tip.label %in% rownames(Data)))){
+            stop('could not match all rownames of Data with all tree tip labels.')
+        } else {
             Data <- Data[PF$tree$tip.label,]
-          }
         }
       }
     }