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add max_density argument

Zuguang Gu authored on 15/06/2022 10:42:56
Showing1 changed files
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@@ -155,4 +155,5 @@ Zuguang Gu <z.gu@dkfz.de>
155 155
 \examples{
156 156
 # There is no example
157 157
 NULL
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+
158 159
 }
Browse code

rename to anno_textbox()

Zuguang Gu authored on 15/06/2022 10:11:58
Showing1 changed files
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@@ -155,5 +155,4 @@ Zuguang Gu <z.gu@dkfz.de>
155 155
 \examples{
156 156
 # There is no example
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 NULL
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-
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 }
Browse code

won't generate color matrix when type=='none'

Zuguang Gu authored on 15/12/2020 12:01:39
Showing1 changed files
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@@ -155,4 +155,5 @@ Zuguang Gu <z.gu@dkfz.de>
155 155
 \examples{
156 156
 # There is no example
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 NULL
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+
158 159
 }
Browse code

translate stats::heatmap() and gplots::heatmap.2()

Zuguang Gu authored on 13/12/2020 20:54:51
Showing1 changed files
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@@ -155,5 +155,4 @@ Zuguang Gu <z.gu@dkfz.de>
155 155
 \examples{
156 156
 # There is no example
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 NULL
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-
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 }
Browse code

various improvements

Zuguang Gu authored on 23/10/2020 16:02:23
Showing1 changed files
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@@ -25,6 +25,7 @@ Make Layout for the Heatmap List
25 25
     annotation_legend_list = list(),
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     align_heatmap_legend = NULL,
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     align_annotation_legend = NULL,
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+    legend_grouping = c("adjusted", "original"),
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     ht_gap = unit(2, "mm"),
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@@ -93,6 +94,7 @@ Make Layout for the Heatmap List
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   \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}}.}
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   \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.}
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   \item{align_annotation_legend}{How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center".}
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+  \item{legend_grouping}{How the legends are grouped. Values should be "adjusted" or "original".}
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   \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.}
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   \item{main_heatmap}{Name or index for the main heatmap.}
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   \item{padding}{Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.}
Browse code

anno_block(): allows to set width and height

Zuguang Gu authored on 29/06/2020 15:54:31
Showing1 changed files
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@@ -23,6 +23,8 @@ Make Layout for the Heatmap List
23 23
     annotation_legend_side = c("right", "left", "bottom", "top"),
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     show_annotation_legend = TRUE,
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     annotation_legend_list = list(),
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+    align_heatmap_legend = NULL,
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+    align_annotation_legend = NULL,
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     ht_gap = unit(2, "mm"),
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... ...
@@ -89,6 +91,8 @@ Make Layout for the Heatmap List
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   \item{annotation_legend_side}{Side of annotation legends.}
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   \item{show_annotation_legend}{Whether show annotation legends.}
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   \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}}.}
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+  \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.}
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+  \item{align_annotation_legend}{How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center".}
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   \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.}
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   \item{main_heatmap}{Name or index for the main heatmap.}
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   \item{padding}{Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.}
Browse code

add use_raster in draw()

jokergoo authored on 29/01/2020 13:14:26
Showing1 changed files
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@@ -65,7 +65,13 @@ Make Layout for the Heatmap List
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     column_km_repeats = NULL,
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     column_split = NULL,
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     width = NULL,
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-    heatmap_width = NULL)
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+    heatmap_width = NULL,
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+    
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+    use_raster = NULL,
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+    raster_device = NULL,
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+    raster_quality = NULL,
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+    raster_device_param = NULL,
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+    raster_resize = NULL)
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 }
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 \arguments{
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@@ -121,6 +127,11 @@ Make Layout for the Heatmap List
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   \item{column_split}{Overwrite the corresponding setting in the main heatmap.}
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   \item{width}{Overwrite the corresponding setting in the main heatmap.}
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   \item{heatmap_width}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{use_raster}{Overwrite the corresponding setting in every heatmap.}
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+  \item{raster_device}{Overwrite the corresponding setting in every heatmap.}
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+  \item{raster_quality}{Overwrite the corresponding setting in every heatmap.}
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+  \item{raster_device_param}{Overwrite the corresponding setting in every heatmap.}
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+  \item{raster_resize}{Overwrite the corresponding setting in every heatmap.}
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 }
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 \details{
Browse code

update

Zuguang Gu authored on 20/10/2019 06:57:30
Showing1 changed files
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@@ -138,4 +138,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
139 139
 # There is no example
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 NULL
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+
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 }
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
Showing1 changed files
1 1
new file mode 100644
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@@ -0,0 +1,141 @@
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+\name{make_layout-HeatmapList-method}
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+\alias{make_layout,HeatmapList-method}
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+\title{
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+Make Layout for the Heatmap List
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+}
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+\description{
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+Make Layout for the Heatmap List
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+}
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+\usage{
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+\S4method{make_layout}{HeatmapList}(object,
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+    
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+    row_title = character(0),
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+    row_title_side = c("left", "right"),
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+    row_title_gp = gpar(fontsize = 14),
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+    column_title = character(0),
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+    column_title_side = c("top", "bottom"),
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+    column_title_gp = gpar(fontsize = 14),
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+    
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+    heatmap_legend_side = c("right", "left", "bottom", "top"),
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+    merge_legends = FALSE,
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+    show_heatmap_legend = TRUE,
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+    heatmap_legend_list = list(),
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+    annotation_legend_side = c("right", "left", "bottom", "top"),
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+    show_annotation_legend = TRUE,
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+    annotation_legend_list = list(),
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+    
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+    ht_gap = unit(2, "mm"),
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+    
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+    main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],
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+    padding = GLOBAL_PADDING,
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+    
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+    auto_adjust = TRUE,
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+    row_dend_side = c("original", "left", "right"),
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+    row_sub_title_side = c("original", "left", "right"),
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+    column_dend_side = c("original", "top", "bottom"),
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+    column_sub_title_side = c("original", "top", "bottom"),
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+    
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+    row_gap = NULL,
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+    cluster_rows = NULL,
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+    cluster_row_slices = NULL,
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+    clustering_distance_rows = NULL,
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+    clustering_method_rows = NULL,
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+    row_dend_width = NULL,
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+    show_row_dend = NULL,
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+    row_dend_reorder = NULL,
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+    row_dend_gp = NULL,
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+    row_order = NULL,
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+    row_km = NULL,
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+    row_km_repeats = NULL,
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+    row_split = NULL,
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+    height = NULL,
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+    heatmap_height = NULL,
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+    
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+    column_gap = NULL,
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+    cluster_columns = NULL,
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+    cluster_column_slices = NULL,
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+    clustering_distance_columns = NULL,
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+    clustering_method_columns = NULL,
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+    column_dend_width = NULL,
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+    show_column_dend = NULL,
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+    column_dend_reorder = NULL,
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+    column_dend_gp = NULL,
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+    column_order = NULL,
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+    column_km = NULL,
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+    column_km_repeats = NULL,
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+    column_split = NULL,
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+    width = NULL,
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+    heatmap_width = NULL)
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+}
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+\arguments{
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+
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+  \item{object}{A \code{\link{HeatmapList-class}} object.}
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+  \item{row_title}{Title on the row.}
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+  \item{row_title_side}{Will the title be put on the left or right of the heatmap list?}
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+  \item{row_title_gp}{Graphic parameters for the row title.}
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+  \item{column_title}{Title on the column.}
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+  \item{column_title_side}{Will the title be put on the top or bottom of the heatmap?}
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+  \item{column_title_gp}{Graphic parameters for the column title.}
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+  \item{heatmap_legend_side}{Side of the heatmap legends.}
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+  \item{merge_legends}{Whether to put heatmap legends and annotation legends together. By default they are put in different viewports.}
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+  \item{show_heatmap_legend}{Whether show heatmap legends.}
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+  \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}}. }
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+  \item{annotation_legend_side}{Side of annotation legends.}
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+  \item{show_annotation_legend}{Whether show annotation legends.}
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+  \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}}.}
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+  \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.}
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+  \item{main_heatmap}{Name or index for the main heatmap.}
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+  \item{padding}{Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.}
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+  \item{auto_adjust}{whether apply automatic adjustment? The auto-adjustment includes turning off dendrograms, titles and row/columns for non-main heatmaps.}
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+  \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?}
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+  \item{row_sub_title_side}{There can be sub titles generated by the splitting of heatmaps. Similar setting as \code{row_dend_side}.}
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+  \item{column_dend_side}{Similar setting as \code{row_dend_side}.}
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+  \item{column_sub_title_side}{Similar setting as \code{row_sub_title_side}.}
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+  \item{row_gap}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{cluster_rows}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{cluster_row_slices}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{clustering_distance_rows}{Overwrite the corresponding setting in the main heatmap.}
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+  \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.}
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+  \item{row_dend_width}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{show_row_dend}{same Overwrite the corresponding setting in the main heatmap.}
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+  \item{row_dend_reorder}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{row_dend_gp}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{row_order}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{row_km}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{row_km_repeats}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{row_split}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{height}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{heatmap_height}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{column_gap}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{cluster_columns}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{cluster_column_slices}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{clustering_distance_columns}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{clustering_method_columns}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{column_dend_width}{column Overwrite the corresponding setting in the main heatmap.}
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+  \item{show_column_dend}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{column_dend_reorder}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{column_dend_gp}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{column_order}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{column_km}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{column_km_repeats}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{column_split}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{width}{Overwrite the corresponding setting in the main heatmap.}
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+  \item{heatmap_width}{Overwrite the corresponding setting in the main heatmap.}
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+
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+}
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+\details{
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+It sets the size of each component of the heatmap list and adjusts graphic
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+parameters for each heatmap if necessary.
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+
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+This function is only for internal use.
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+}
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+\value{
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+A \code{\link{HeatmapList-class}} object in which settings for all heatmap are adjusted.
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+}
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+\author{
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+Zuguang Gu <z.gu@dkfz.de>
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+}
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+\examples{
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+# There is no example
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+NULL
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+}