@@ -6,7 +6,7 @@ Version: 1.31.0

 Date: 2015-12-25

 Author: Diego Diez

 Depends: R (>= 2.10), igraph (>= 1.0)

-Imports: AnnotationDbi, DBI, RSQLite

+Imports: methods, AnnotationDbi, DBI, RSQLite

 Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt,

         knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db,

         ggplot2

@@ -8,6 +8,7 @@ importMethodsFrom(DBI,

                   "fetch")

 importFrom("grDevices", "col2rgb", "colors", "grey.colors")

+importFrom("methods", "is")

 importFrom(

   "graphics",

   "abline",

@@ -137,13 +137,12 @@ annotateTRM = function(g, target) {

   else

     default

 }

-

 plotTRM = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE, normalize.layout=TRUE) {

-  if(class(layout) == "function")

+  if(is(layout, "function"))

     l = layout(g)

   else

-    l = layout

+    l = as.matrix(layout)

   # normalize layout.

   if(normalize.layout)