@@ -1,5 +1,5 @@

 Package: Gviz

-Version: 1.2.0

+Version: 1.2.1

 Title: Plotting data and annotation information along genomic coordinates

 Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou>

 Maintainer: Florian Hahne <florian.hahne@novartis.com>

@@ -2354,6 +2354,18 @@ setMethod("drawGD", signature("AlignedReadTrack"), function(GdObject, minBase, m

     return(coords)

 }

+

+## A more generic method to come up with colors for chromosome bands that still relies a bit on biovizBase

+.getBioColorIdeo <- function(type){

+    type <- as.character(type)

+    ocols <- getBioColor("CYTOBAND")

+    cols <- c(ocols[c("gneg", "stalk", "acen")], gpos=unname(ocols["gpos100"]), gvar=unname(ocols["gpos100"]))

+    gpcols <- unique(grep("gpos", type, value=TRUE))

+    crmp <- colorRampPalette(c(cols["gneg"], cols["gpos"]))(100)

+    posCols <- setNames(crmp[as.integer(gsub("gpos", "", gpcols))], gpcols)

+    return(c(cols, posCols))

+}

+

 ## The actual drawing method

 setMethod("drawGD", signature("IdeogramTrack"), function(GdObject, minBase, maxBase, prepare=FALSE, ...) {

     imageMap(GdObject) <- NULL

@@ -2401,7 +2413,7 @@ setMethod("drawGD", signature("IdeogramTrack"), function(GdObject, minBase, maxB

         grid.rect(minBase/len, 0.1, width=min(1,(maxBase-minBase)/len), height=0.8, just=c("left","bottom"),

                   gp=gpar(col="transparent", fill=fill))

     ## Color mapping for the bands taken from the biovizBase package

-    cols <- getBioColor("CYTOBAND")

+    cols <- .getBioColorIdeo(values(GdObject)$type)

     vals <- data.frame(values(GdObject), col=cols[as.character(values(GdObject)$type)], stringsAsFactors=FALSE)

     ## For the rounded caps we need  to figure out the overlap with existing bands for proper coloring

     bevel <- 0.02