@@ -9,7 +9,7 @@ Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

 Imports: circlize (>= 0.4.1), GetoptLong, colorspace,

     RColorBrewer, GlobalOptions (>= 0.1.0)

 Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust, 

-    dendsort, HilbertCurve, Cairo, png, jpeg, tiff, fastcluster,

+    dendsort, HilbertCurve (>= 1.11.1), Cairo, png, jpeg, tiff, fastcluster,

     dendextend (>= 1.0.1), grImport, grImport2, rsvg, glue

 VignetteBuilder: knitr

 Description: Complex heatmaps are efficient to visualize associations 

@@ -42,8 +42,6 @@ S3method("length", "HeatmapAnnotation")

 export("length.HeatmapAnnotation")

 S3method("length", "HeatmapList")

 export("length.HeatmapList")

-S3method("merge", "dendrogram")

-export("merge.dendrogram")

 S3method("names", "HeatmapAnnotation")

 export("names.HeatmapAnnotation")

 S3method("names", "HeatmapList")

@@ -154,6 +152,7 @@ export("is_abs_unit")

 export("list_component")

 export("max_text_height")

 export("max_text_width")

+export("merge_dendrogram")

 export("oncoPrint")

 export("packLegend")

 export("pindex")

@@ -129,14 +129,23 @@ HeatmapAnnotation = function(...,

 	n_anno = 0

 	#### check system calls ####

+

+	# HeatmapAnnotation is either called by `HeatmapAnnotation()` or by `rowAnnotation()`/`columnAnnotation()`

 	sc = sys.calls()

-	for(i in seq_along(sc)) {

-		scl = as.list(sc[[i]])

+	nsc = length(sc)

+	if(nsc == 1) {

+		scl = as.list(sc[[1]])

+		arg_list = scl[-1]

+	} else {

+		scl = as.list(sc[[nsc-1]])

 		if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {

 			arg_list = scl[-1]

-			break

+		} else {

+			scl = as.list(sc[[nsc]])

+			arg_list = scl[-1]

 		}

 	}

+

     called_args = names(arg_list)

     anno_args = setdiff(called_args, fun_args)

     if(any(anno_args == "")) stop("annotations should have names.")

@@ -80,7 +80,7 @@ Heatmap(matrix, col, name,

     show_heatmap_legend = TRUE,

     heatmap_legend_param = list(title = name),

-    use_raster = nrow(matrix) > 2000 || ncol(matrix) > 2000,

+    use_raster = (nrow(matrix) > 2000 && ncol(matrix) > 1) || (ncol(matrix) > 2000 && nrow(matrix) > 1),

     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

     raster_quality = 2,

     raster_device_param = list(),

@@ -18,7 +18,7 @@ cluster_within_group(mat, factor)

 \details{

 The clustering is firstly applied in each group, then clustering is applied

 to group means. The within-group dendrograms and between-group dendrogram

-are finally connected by \code{\link{merge.dendrogram}}.

+are finally connected by \code{\link{merge_dendrogram}}.

 In the final dendrogram, the within group dendrograms are enforced to be 

 flat lines to emphasize that the within group dendrograms have no sense to 

similarity index 80%

rename from man/merge.dendrogram.rd

rename to man/merge_dendrogram.rd

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

-\name{merge.dendrogram}

-\alias{merge.dendrogram}

+\name{merge_dendrogram}

+\alias{merge_dendrogram}

 \title{

 Merge Dendrograms

 }

@@ -7,7 +7,7 @@ Merge Dendrograms

 Merge Dendrograms

 }

 \usage{

-\method{merge}{dendrogram}(x, y, only_parent = FALSE, ...)

+merge_dendrogram(x, y, only_parent = FALSE, ...)

 }

 \arguments{

@@ -28,10 +28,10 @@ dend1 = as.dendrogram(hclust(dist(m1)))

 dend2 = as.dendrogram(hclust(dist(m2)))

 dend3 = as.dendrogram(hclust(dist(m3)))

 dend_p = as.dendrogram(hclust(dist(rbind(colMeans(m1), colMeans(m2), colMeans(m3)))))

-dend_m = merge(dend_p, list(dend1, dend2, dend3))

+dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3))

 grid.dendrogram(dend_m, test = TRUE)

-dend_m = merge(dend_p, list(dend1, dend2, dend3), only_parent = TRUE)

+dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3), only_parent = TRUE)

 grid.dendrogram(dend_m, test = TRUE)

 require(dendextend)

@@ -39,6 +39,6 @@ dend1 = color_branches(dend1, k = 1, col = "red")

 dend2 = color_branches(dend2, k = 1, col = "blue")

 dend3 = color_branches(dend3, k = 1, col = "green")

 dend_p = color_branches(dend_p, k = 1, col = "orange")

-dend_m = merge(dend_p, list(dend1, dend2, dend3))

+dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3))

 grid.dendrogram(dend_m, test = TRUE)

 }