@@ -155,4 +155,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -155,5 +155,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -155,4 +155,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -155,5 +155,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -25,6 +25,7 @@ Make Layout for the Heatmap List

     annotation_legend_list = list(),

     align_heatmap_legend = NULL,

     align_annotation_legend = NULL,

+    legend_grouping = c("adjusted", "original"),

     ht_gap = unit(2, "mm"),

@@ -93,6 +94,7 @@ Make Layout for the Heatmap List

   \item{annotation_legend_list}{A list of self-defined legends, should be wrapped into a list of \code{\link[grid:grid.grob]{grob}} objects. Normally they are constructed by \code{\link{Legend}}.}

   \item{align_heatmap_legend}{How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is \code{NULL}, it automatically picks the proper value from the three options.}

   \item{align_annotation_legend}{How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center".}

+  \item{legend_grouping}{How the legends are grouped. Values should be "adjusted" or "original".}

   \item{ht_gap}{Gap between heatmaps, should be a \code{\link[grid]{unit}} object. It can be a vector of length 1 or the number of heamtaps/annotations.}

   \item{main_heatmap}{Name or index for the main heatmap.}

   \item{padding}{Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.}

@@ -23,6 +23,8 @@ Make Layout for the Heatmap List

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

     show_annotation_legend = TRUE,

     annotation_legend_list = list(),

+    align_heatmap_legend = NULL,

+    align_annotation_legend = NULL,

     ht_gap = unit(2, "mm"),

@@ -89,6 +91,8 @@ Make Layout for the Heatmap List

   \item{annotation_legend_side}{Side of annotation legends.}

   \item{show_annotation_legend}{Whether show annotation legends.}

   \item{annotation_legend_list}{A list of self-defined legends, should be wrapped into a list of \code{\link[grid:grid.grob]{grob}} objects. Normally they are constructed by \code{\link{Legend}}.}

+  \item{align_heatmap_legend}{How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is \code{NULL}, it automatically picks the proper value from the three options.}

+  \item{align_annotation_legend}{How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center".}

   \item{ht_gap}{Gap between heatmaps, should be a \code{\link[grid]{unit}} object. It can be a vector of length 1 or the number of heamtaps/annotations.}

   \item{main_heatmap}{Name or index for the main heatmap.}

   \item{padding}{Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.}

@@ -65,7 +65,13 @@ Make Layout for the Heatmap List

     column_km_repeats = NULL,

     column_split = NULL,

     width = NULL,

-    heatmap_width = NULL)

+    heatmap_width = NULL,

+    

+    use_raster = NULL,

+    raster_device = NULL,

+    raster_quality = NULL,

+    raster_device_param = NULL,

+    raster_resize = NULL)

 }

 \arguments{

@@ -121,6 +127,11 @@ Make Layout for the Heatmap List

   \item{column_split}{Overwrite the corresponding setting in the main heatmap.}

   \item{width}{Overwrite the corresponding setting in the main heatmap.}

   \item{heatmap_width}{Overwrite the corresponding setting in the main heatmap.}

+  \item{use_raster}{Overwrite the corresponding setting in every heatmap.}

+  \item{raster_device}{Overwrite the corresponding setting in every heatmap.}

+  \item{raster_quality}{Overwrite the corresponding setting in every heatmap.}

+  \item{raster_device_param}{Overwrite the corresponding setting in every heatmap.}

+  \item{raster_resize}{Overwrite the corresponding setting in every heatmap.}

 }

 \details{

@@ -138,4 +138,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

new file mode 100644

@@ -0,0 +1,141 @@

+\name{make_layout-HeatmapList-method}

+\alias{make_layout,HeatmapList-method}

+\title{

+Make Layout for the Heatmap List

+}

+\description{

+Make Layout for the Heatmap List

+}

+\usage{

+\S4method{make_layout}{HeatmapList}(object,

+    

+    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"),

+    merge_legends = FALSE,

+    show_heatmap_legend = TRUE,

+    heatmap_legend_list = list(),

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

+    show_annotation_legend = TRUE,

+    annotation_legend_list = list(),

+    

+    ht_gap = unit(2, "mm"),

+    

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

+    padding = GLOBAL_PADDING,

+    

+    auto_adjust = TRUE,

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

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

+    column_dend_side = c("original", "top", "bottom"),

+    column_sub_title_side = c("original", "top", "bottom"),

+    

+    row_gap = NULL,

+    cluster_rows = NULL,

+    cluster_row_slices = NULL,

+    clustering_distance_rows = NULL,

+    clustering_method_rows = NULL,

+    row_dend_width = NULL,

+    show_row_dend = NULL,

+    row_dend_reorder = NULL,

+    row_dend_gp = NULL,

+    row_order = NULL,

+    row_km = NULL,

+    row_km_repeats = NULL,

+    row_split = NULL,

+    height = NULL,

+    heatmap_height = NULL,

+    

+    column_gap = NULL,

+    cluster_columns = NULL,

+    cluster_column_slices = NULL,

+    clustering_distance_columns = NULL,

+    clustering_method_columns = NULL,

+    column_dend_width = NULL,

+    show_column_dend = NULL,

+    column_dend_reorder = NULL,

+    column_dend_gp = NULL,

+    column_order = NULL,

+    column_km = NULL,

+    column_km_repeats = NULL,

+    column_split = NULL,

+    width = NULL,

+    heatmap_width = NULL)

+}

+\arguments{

+

+  \item{object}{A \code{\link{HeatmapList-class}} object.}

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

+  \item{row_title_side}{Will the title be put on the left or right of the heatmap list?}

+  \item{row_title_gp}{Graphic parameters for the row title.}

+  \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 the column title.}

+  \item{heatmap_legend_side}{Side of the heatmap legends.}

+  \item{merge_legends}{Whether to put heatmap legends and annotation legends together. By default they are put in different viewports.}

+  \item{show_heatmap_legend}{Whether show heatmap legends.}

+  \item{heatmap_legend_list}{A list of self-defined legends, should be wrapped into a list of \code{\link[grid:grid.grob]{grob}} objects. Normally they are constructed by \code{\link{Legend}}. }

+  \item{annotation_legend_side}{Side of annotation legends.}

+  \item{show_annotation_legend}{Whether show annotation legends.}

+  \item{annotation_legend_list}{A list of self-defined legends, should be wrapped into a list of \code{\link[grid:grid.grob]{grob}} objects. Normally they are constructed by \code{\link{Legend}}.}

+  \item{ht_gap}{Gap between heatmaps, should be a \code{\link[grid]{unit}} object. It can be a vector of length 1 or the number of heamtaps/annotations.}

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

+  \item{padding}{Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.}

+  \item{auto_adjust}{whether apply automatic adjustment? The auto-adjustment includes turning off dendrograms, titles and row/columns for non-main heatmaps.}

+  \item{row_dend_side}{If auto-adjustment is on, to put the row dendrograms of the main heatmap to the most left side of the heatmap list or the most right side?}

+  \item{row_sub_title_side}{There can be sub titles generated by the splitting of heatmaps. Similar setting as \code{row_dend_side}.}

+  \item{column_dend_side}{Similar setting as \code{row_dend_side}.}

+  \item{column_sub_title_side}{Similar setting as \code{row_sub_title_side}.}

+  \item{row_gap}{Overwrite the corresponding setting in the main heatmap.}

+  \item{cluster_rows}{Overwrite the corresponding setting in the main heatmap.}

+  \item{cluster_row_slices}{Overwrite the corresponding setting in the main heatmap.}

+  \item{clustering_distance_rows}{Overwrite the corresponding setting in the main heatmap.}

+  \item{clustering_method_rows}{Overwrite the corresponding setting in the main heatmap.same setting as in \code{\link{Heatmap}}, if it is specified, \code{clustering_method_rows} in main heatmap is ignored.}

+  \item{row_dend_width}{Overwrite the corresponding setting in the main heatmap.}

+  \item{show_row_dend}{same Overwrite the corresponding setting in the main heatmap.}

+  \item{row_dend_reorder}{Overwrite the corresponding setting in the main heatmap.}

+  \item{row_dend_gp}{Overwrite the corresponding setting in the main heatmap.}

+  \item{row_order}{Overwrite the corresponding setting in the main heatmap.}

+  \item{row_km}{Overwrite the corresponding setting in the main heatmap.}

+  \item{row_km_repeats}{Overwrite the corresponding setting in the main heatmap.}

+  \item{row_split}{Overwrite the corresponding setting in the main heatmap.}

+  \item{height}{Overwrite the corresponding setting in the main heatmap.}

+  \item{heatmap_height}{Overwrite the corresponding setting in the main heatmap.}

+  \item{column_gap}{Overwrite the corresponding setting in the main heatmap.}

+  \item{cluster_columns}{Overwrite the corresponding setting in the main heatmap.}

+  \item{cluster_column_slices}{Overwrite the corresponding setting in the main heatmap.}

+  \item{clustering_distance_columns}{Overwrite the corresponding setting in the main heatmap.}

+  \item{clustering_method_columns}{Overwrite the corresponding setting in the main heatmap.}

+  \item{column_dend_width}{column Overwrite the corresponding setting in the main heatmap.}

+  \item{show_column_dend}{Overwrite the corresponding setting in the main heatmap.}

+  \item{column_dend_reorder}{Overwrite the corresponding setting in the main heatmap.}

+  \item{column_dend_gp}{Overwrite the corresponding setting in the main heatmap.}

+  \item{column_order}{Overwrite the corresponding setting in the main heatmap.}

+  \item{column_km}{Overwrite the corresponding setting in the main heatmap.}

+  \item{column_km_repeats}{Overwrite the corresponding setting in the main heatmap.}

+  \item{column_split}{Overwrite the corresponding setting in the main heatmap.}

+  \item{width}{Overwrite the corresponding setting in the main heatmap.}

+  \item{heatmap_width}{Overwrite the corresponding setting in the main heatmap.}

+

+}

+\details{

+It sets the size of each component of the heatmap list and adjusts graphic

+parameters for each heatmap if necessary.

+

+This function is only for internal use.

+}

+\value{

+A \code{\link{HeatmapList-class}} object in which settings for all heatmap are adjusted.

+}

+\author{

+Zuguang Gu <z.gu@dkfz.de>

+}

+\examples{

+# There is no example

+NULL

+}