@@ -462,10 +462,12 @@ function(object, GStoGenes, numPerm, Pw, PwNull)

 #' @param data the original data as a matrix

 #' @param patternPalette a vector indicating what color should be used

 #' for each pattern

+#' @param patternMarkers pattern markers to be plotted, as generated by the 

+#' patternMarkers function

 #' @param sampleNames names of the samples to use for labeling 

 #' @param samplePalette  a vector indicating what color should be used

 #' for each sample

-#' @param colDenogram logical indicating whether to display sample denogram

+#' @param colDendrogram logical indicating whether to display sample dendrogram

 #' @param heatmapCol pallelet giving color scheme for heatmap

 #' @param scale character indicating if the values should be centered and scaled

 #' in either the row direction or the column direction, or none. The

@@ -476,8 +478,8 @@ function(object, GStoGenes, numPerm, Pw, PwNull)

 #' @importFrom gplots bluered

 #' @importFrom gplots heatmap.2

 #' @importFrom stats hclust as.dist cor

-plotPatternMarkers <- function(object, data, patternPalette, sampleNames,

-samplePalette=NULL, heatmapCol=bluered, colDenogram=TRUE, scale="row", ...)

+plotPatternMarkers <- function(object, data, patternMarkers, patternPalette, sampleNames,

+samplePalette=NULL, heatmapCol=bluered, colDendrogram=TRUE, scale="row", ...)

 {

     if (is.null(samplePalette))

         samplePalette <- rep("black", ncol(data))

@@ -487,10 +489,10 @@ samplePalette=NULL, heatmapCol=bluered, colDenogram=TRUE, scale="row", ...)

     names(patternCols) <- unlist(patternMarkers)

     for (i in 1:length(patternMarkers))

     {

-        patternCols[patternMarkers[[i]]] <- patternPalette[i]

+        patternCols[unlist(patternMarkers$PatternMarkers[[i]])] <- patternPalette[i]

     }

-    gplots::heatmap.2(as.matrix(data[unlist(patternMarkers),],...),

+    gplots::heatmap.2(as.matrix(data[unlist(patternMarkers$PatternMarkers),],),

         symkey=FALSE,

         symm=FALSE, 

         scale=scale,

@@ -498,9 +500,9 @@ samplePalette=NULL, heatmapCol=bluered, colDenogram=TRUE, scale="row", ...)

         distfun=function(x) as.dist((1-cor(t(x)))/2),

         hclustfun=function(x) stats::hclust(x,method="average"),

         Rowv=FALSE,

-        Colv=colDenogram,

+        Colv=colDendrogram,

         trace='none',

-        RowSideColors = as.character(patternCols[unlist(patternMarkers)]),

+        RowSideColors = as.character(patternCols[unlist(patternMarkers$PatternMarkers)]),

         labCol= sampleNames,

         cexCol=0.8,

         ColSideColors=as.character(samplePalette),