@@ -1,114 +1,114 @@

-export(column_anno_histogram)

-export(anno_boxplot)

-exportMethods(column_order)

+export('+.AdditiveUnit')

+export(AdditiveUnit)

 export(ColorMapping)

+export(Heatmap)

 export(HeatmapAnnotation)

+export(HeatmapList)

+export(SingleAnnotation)

+export(anno_barplot)

+export(anno_boxplot)

+export(anno_density)

+export(anno_histogram)

+export(anno_link)

+export(anno_points)

+export(anno_text)

+export(columnAnnotation)

+export(column_anno_barplot)

 export(column_anno_boxplot)

-export(selectArea)

-export(row_anno_barplot)

-export(Heatmap)

-export(row_anno_points)

+export(column_anno_density)

+export(column_anno_histogram)

+export(column_anno_link)

+export(column_anno_points)

 export(column_anno_text)

-export(decorate_row_dend)

-export(decorate_column_dend)

-exportMethods(draw)

-export(unify_mat_list)

-exportMethods(draw_heatmap_body)

-exportMethods(color_mapping_legend)

-exportMethods(prepare)

 export(decorate_annotation)

-exportMethods(map_to_colors)

+export(decorate_column_dend)

+export(decorate_column_names)

+export(decorate_column_title)

+export(decorate_dend)

 export(decorate_dimnames)

-export(column_anno_points)

-exportMethods(component_height)

-export(row_anno_text)

-exportClasses(SingleAnnotation)

-export(SingleAnnotation)

-export(oncoPrint)

-exportClasses(AdditiveUnit)

-export(AdditiveUnit)

-export(max_text_height)

+export(decorate_heatmap_body)

+export(decorate_row_dend)

+export(decorate_row_names)

+export(decorate_row_title)

+export(decorate_title)

+export(densityHeatmap)

+export(dist2)

 export(enhanced_basicplot)

-exportMethods(annotation_legend_size)

-exportMethods(row_order)

-export(AdditiveUnit)

-exportMethods(draw_heatmap_list)

-export(row_anno_density)

+export(grid.dendrogram)

+export(ht_global_opt)

 export(is_abs_unit)

-export(dist2)

-export(decorate_heatmap_body)

-exportMethods(draw_heatmap_legend)

-exportMethods(add_heatmap)

-export(anno_barplot)

-exportMethods(row_dend)

-export(row_anno_boxplot)

+export(max_text_height)

 export(max_text_width)

-export(anno_link)

-exportMethods(make_layout)

-export(decorate_row_title)

-export(anno_histogram)

+export(oncoPrint)

 export(plotDataFrame)

-exportMethods(draw_dimnames)

+export(rowAnnotation)

+export(row_anno_barplot)

+export(row_anno_boxplot)

+export(row_anno_density)

+export(row_anno_histogram)

+export(row_anno_link)

+export(row_anno_points)

+export(row_anno_text)

+export(selectArea)

+export(unify_mat_list)

+exportClasses(AdditiveUnit)

+export(AdditiveUnit)

 exportClasses(ColorMapping)

 export(ColorMapping)

+exportClasses(Heatmap)

+export(Heatmap)

 exportClasses(HeatmapAnnotation)

 export(HeatmapAnnotation)

-export(anno_points)

-exportMethods(draw_title)

-export(ht_global_opt)

-export('+.AdditiveUnit')

-export(decorate_column_names)

-export(column_anno_barplot)

-export(densityHeatmap)

-exportMethods(heatmap_legend_size)

 exportClasses(HeatmapList)

 export(HeatmapList)

-export(column_anno_density)

-exportClasses(Heatmap)

-export(Heatmap)

-exportMethods(draw_annotation_legend)

-exportMethods(column_dend)

-exportMethods(set_component_height)

-export(row_anno_link)

-exportMethods(make_column_cluster)

-export(HeatmapList)

-exportMethods(draw_annotation)

+exportClasses(SingleAnnotation)

 export(SingleAnnotation)

-export(row_anno_histogram)

-exportMethods(get_color_mapping_list)

-exportMethods(make_row_cluster)

+exportMethods(add_heatmap)

+exportMethods(annotation_legend_size)

+exportMethods(color_mapping_legend)

+exportMethods(column_dend)

+exportMethods(column_order)

+exportMethods(component_height)

 exportMethods(component_width)

-export(decorate_column_title)

+exportMethods(draw)

+exportMethods(draw_annotation)

+exportMethods(draw_annotation_legend)

 exportMethods(draw_dend)

+exportMethods(draw_dimnames)

+exportMethods(draw_heatmap_body)

+exportMethods(draw_heatmap_legend)

+exportMethods(draw_heatmap_list)

+exportMethods(draw_title)

+exportMethods(get_color_mapping_list)

 exportMethods(get_color_mapping_param_list)

-export(grid.dendrogram)

-export(decorate_title)

-export(decorate_dend)

-export(rowAnnotation)

-export(column_anno_link)

-export(columnAnnotation)

-export(decorate_row_names)

-export(anno_text)

-export(anno_density)

+exportMethods(heatmap_legend_size)

+exportMethods(make_column_cluster)

+exportMethods(make_layout)

+exportMethods(make_row_cluster)

+exportMethods(map_to_colors)

+exportMethods(prepare)

+exportMethods(row_dend)

+exportMethods(row_order)

+exportMethods(set_component_height)

+import(grDevices)

+import(graphics)

 import(grid)

-importFrom("methods", setClass)

-importFrom("methods", setMethod)

-importFrom("methods", setGeneric)

+import(stats)

+importFrom("GetoptLong", qq)

+importFrom("GetoptLong", qq.options)

+importFrom("GetoptLong", qqcat)

+importFrom("GlobalOptions", setGlobalOptions)

+importFrom("RColorBrewer", brewer.pal)

 importFrom("circlize", colorRamp2)

 importFrom("circlize", rand_color)

 importFrom("circlize", smartAlign)

-importFrom("GetoptLong", qq)

-importFrom("GetoptLong", qqcat)

-importFrom("GetoptLong", qq.options)

-importFrom("colorspace", rainbow_hcl)

 importFrom("colorspace", diverge_hcl)

-importFrom("RColorBrewer", brewer.pal)

+importFrom("colorspace", rainbow_hcl)

+importFrom("dendextend", "labels<-")

 importFrom("dendextend", get_branches_heights)

 importFrom("dendextend", nnodes)

-importFrom("dendextend", "labels<-")

-import(graphics)

-import(stats)

-import(grDevices)

-importFrom("GlobalOptions", setGlobalOptions)

+importFrom("methods", setClass)

+importFrom("methods", setGeneric)

+importFrom("methods", setMethod)

@@ -4,6 +4,8 @@ CHANGES in VERSION 1.9.5

   of column names when there are bottom annotations.

 * fixed a bug that character NA values can not to assigned with na_col

 * extra character 'at' and 'labels' in legends will be removed automatically

+* all arguments which are passed to `make_layout()` are all explicitly put

+  in `draw()` instead of using ...

 =============================

@@ -591,6 +591,22 @@ setMethod(f = "make_layout",

 # -object a `HeatmapList-class` object

 # -padding padding of the plot. Elements correspond to bottom, left, top, right paddings.

 # -newpage whether create a new page for the graphics.

+# -row_title title on the row.

+# -row_title_side will the title be put on the left or right of the heatmap.

+# -row_title_gp graphic parameters for drawing text.

+# -column_title title on the column.

+# -column_title_side will the title be put on the top or bottom of the heatmap.

+# -column_title_gp graphic parameters for drawing text.

+# -heatmap_legend_side side of the heatmap legend.

+# -show_heatmap_legend whether show heatmap legend.

+# -heatmap_legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

+# -annotation_legend_side side of annotation legend.

+# -show_annotation_legend whether show annotation legend.

+# -annotation_legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

+# -gap gap between heatmaps, should be a `grid::unit` object.

+# -main_heatmap name or index for the main heatmap

+# -row_dend_side if auto adjust, where to put the row dendrograms for the main heatmap

+# -row_sub_title_side if auto adjust, where to put sub row titles for the main heatmap

 # -... pass to `make_layout,HeatmapList-method`

 #

 # == detail

@@ -610,7 +626,22 @@ setMethod(f = "draw",

     definition = function(object, 

         padding = unit(c(2, 2, 2, 2), "mm"), 

         newpage = TRUE,

-        ...) {

+        row_title = character(0), 

+        row_title_side = c("left", "right"), 

+        row_title_gp = gpar(fontsize = 14),

+        column_title = character(0), 

+        column_title_side = c("top", "bottom"), 

+        column_title_gp = gpar(fontsize = 14), 

+        heatmap_legend_side = c("right", "left", "bottom", "top"), 

+        show_heatmap_legend = TRUE, 

+        heatmap_legend_list = list(),

+        annotation_legend_side = c("right", "left", "bottom", "top"), 

+        show_annotation_legend = TRUE, 

+        annotation_legend_list = list(),

+        gap = unit(3, "mm"), 

+        main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

+        row_dend_side = c("original", "left", "right"),

+        row_sub_title_side = c("original", "left", "right"), ...) {

     l = sapply(object@ht_list, inherits, "Heatmap")

     if(! any(l)) {

@@ -624,7 +655,12 @@ setMethod(f = "draw",

         grid.newpage()

     }

-    object = make_layout(object, ...)

+    object = make_layout(object, row_title = row_title, row_title_gp = row_title_gp, row_title_side = row_title_side,

+        column_title = column_title, column_title_side = column_title_side, column_title_gp = column_title_gp,

+        heatmap_legend_side = heatmap_legend_side, show_heatmap_legend = show_heatmap_legend, heatmap_legend_list = heatmap_legend_list,

+        annotation_legend_side = annotation_legend_side, show_annotation_legend = show_annotation_legend,

+        annotation_legend_list = annotation_legend_list, gap = gap, main_heatmap = main_heatmap, row_dend_side = row_dend_side,

+        row_sub_title_side = row_sub_title_side, ...)

     if(length(padding) == 1) {

         padding = rep(padding, 4)

@@ -10,13 +10,44 @@ Draw a list of heatmaps

 \S4method{draw}{HeatmapList}(object,

     padding = unit(c(2, 2, 2, 2), "mm"),

     newpage = TRUE,

-    ...)

+    row_title = character(0),

+    row_title_side = c("left", "right"),

+    row_title_gp = gpar(fontsize = 14),

+    column_title = character(0),

+    column_title_side = c("top", "bottom"),

+    column_title_gp = gpar(fontsize = 14),

+    heatmap_legend_side = c("right", "left", "bottom", "top"),

+    show_heatmap_legend = TRUE,

+    heatmap_legend_list = list(),

+    annotation_legend_side = c("right", "left", "bottom", "top"),

+    show_annotation_legend = TRUE,

+    annotation_legend_list = list(),

+    gap = unit(3, "mm"),

+    main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

+    row_dend_side = c("original", "left", "right"),

+    row_sub_title_side = c("original", "left", "right"), ...)

 }

 \arguments{

   \item{object}{a \code{\link{HeatmapList-class}} object}

   \item{padding}{padding of the plot. Elements correspond to bottom, left, top, right paddings.}

   \item{newpage}{whether create a new page for the graphics.}

+  \item{row_title}{title on the row.}

+  \item{row_title_side}{will the title be put on the left or right of the heatmap.}

+  \item{row_title_gp}{graphic parameters for drawing text.}

+  \item{column_title}{title on the column.}

+  \item{column_title_side}{will the title be put on the top or bottom of the heatmap.}

+  \item{column_title_gp}{graphic parameters for drawing text.}

+  \item{heatmap_legend_side}{side of the heatmap legend.}

+  \item{show_heatmap_legend}{whether show heatmap legend.}

+  \item{heatmap_legend_list}{a list of self-defined legend, should be wrapped into \code{\link[grid]{grob}} objects.}

+  \item{annotation_legend_side}{side of annotation legend.}

+  \item{show_annotation_legend}{whether show annotation legend.}

+  \item{annotation_legend_list}{a list of self-defined legend, should be wrapped into \code{\link[grid]{grob}} objects.}

+  \item{gap}{gap between heatmaps, should be a \code{\link[grid]{unit}} object.}

+  \item{main_heatmap}{name or index for the main heatmap}

+  \item{row_dend_side}{if auto adjust, where to put the row dendrograms for the main heatmap}

+  \item{row_sub_title_side}{if auto adjust, where to put sub row titles for the main heatmap}

   \item{...}{pass to \code{\link{make_layout,HeatmapList-method}}}

 }

@@ -77,7 +77,7 @@ From left to right, heatmaps are:

 8. overlapping between DMRs and enhancers (Color shows how much the DMR is covered by the enhancers).

-```{r, fig.width = 10, fig.height = 8, echo = FALSE}

+```{r, fig.width = 10, fig.height = 8, echo = FALSE, results = "hide"}

 library(circlize)

 library(RColorBrewer)