[Vegan-commits] r2435 - pkg/vegan/R

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2013-02-13 17:52:34 +0100 (Wed, 13 Feb 2013)
New Revision: 2435

Modified:
   pkg/vegan/R/tabasco.R
Log:
tabasco did not return (invisibly) correct indices when dendrograms were used

Modified: pkg/vegan/R/tabasco.R
===================================================================
--- pkg/vegan/R/tabasco.R	2013-02-13 14:24:23 UTC (rev 2434)
+++ pkg/vegan/R/tabasco.R	2013-02-13 16:52:34 UTC (rev 2435)
@@ -19,20 +19,19 @@
         else if (inherits(use, "hclust")) {
             if (!is.null(site.ind))
                 stop("'hclust' tree cannot be 'use'd with 'site.ind'")
-            site.ind <- seq_len(nrow(x))
+            site.ind <- use$order
             if (is.null(sp.ind)) 
-                sp.ind <- order(wascores(order(use$order), x))
+                sp.ind <- order(wascores(order(site.ind), x))
             Colv <- as.dendrogram(use)
         }
         else if (inherits(use, "dendrogram")) {
             if (!is.null(site.ind))
                 stop("'dendrogram' cannot be 'use'd with 'site.ind'")
             site.ind <- seq_len(nrow(x))
-            o <- seq_len(nrow(x))
-            names(o) <- rownames(x)
-            o <- o[labels(use)]
+            names(site.ind) <- rownames(x)
+            site.ind <- site.ind[labels(use)]
             if (is.null(sp.ind)) 
-                sp.ind <- order(wascores(order(o), x))
+                sp.ind <- order(wascores(order(site.ind), x))
             Colv <- use
         }
         else if (is.list(use)) {
@@ -59,6 +58,8 @@
             sp.ind <- as.dendrogram(sp.ind)
         Rowv <- sp.ind
         sp.ind <- seq_len(ncol(x))
+        names(sp.ind) <- colnames(x)
+        sp.ind <- sp.ind[labels(Rowv)]
     }
     if (!is.null(sp.ind) && is.logical(sp.ind))
         sp.ind <- (1:ncol(x))[sp.ind]
@@ -69,7 +70,7 @@
     if (is.null(site.ind)) 
         site.ind <- 1:nrow(x)
     if (!missing(select)) {
-        if (inherits(use, c("hclust", "dendrogram")))
+        if (!is.na(Colv))
             stop("sites cannot be 'select'ed with dendrograms or hclust trees")
         if (!is.logical(select))
             select <- sort(site.ind) %in% select
@@ -81,9 +82,19 @@
         stake <- colSums(x[site.ind, ]) > 0
     }
     sp.ind <- sp.ind[stake[sp.ind]]
-    x <- x[site.ind, sp.ind]
-    x <- as.matrix(x)
-    x <- t(x)
+    ## heatmap will reorder items by dendrogram so that we need to
+    ## give indices in the unsorted order if rows or columns have a
+    ## dendrogram
+    if (is.na(Colv[1]))
+        rind <- site.ind
+    else
+        rind <- sort(site.ind)
+    if (is.na(Rowv[1]))
+        cind <- sp.ind
+    else
+        cind <- sort(sp.ind)
+    ## we assume t() changes data.frame to a matrix
+    x <- t(x[rind, cind])
     sp.nam <- rownames(x)
     sp.len <- max(nchar(sp.nam))
     heatmap((max(x) - x), Rowv, Colv,  scale = "none", ...)