Browse code

set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
Showing131 changed files

... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES in VERSION 1.99.5
2 2
 
3 3
 * add `UpSet()` and some related functions to make Upset plots
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+* fixed bugs of drawing legends
4 5
 
5 6
 ========================
6 7
 
... ...
@@ -285,7 +285,11 @@ setMethod(f = "color_mapping_legend",
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 	e = environment()
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 	if(!is.null(param)) {
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 		for(nm in names(param)) {
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-			assign(nm, param[[nm]], envir = e)
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+			if(nm == "direction") {
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+				assign("legend_direction", param[[nm]], envir = e)
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+			} else {
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+				assign(nm, param[[nm]], envir = e)
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+			}
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 		}
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 	}
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@@ -394,6 +394,7 @@ Heatmap = function(matrix, col, name,
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             show_row_dend = FALSE
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         }
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         row_dend_reorder = FALSE
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+        cluster_row_slices = FALSE
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398 399
         if("clustering_distance_columns" %in% called_args) {
399 400
         } else if(inherits(cluster_columns, c("dendrogram", "hclust"))) {
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@@ -402,6 +403,7 @@ Heatmap = function(matrix, col, name,
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             show_column_dend = FALSE
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         }
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         column_dend_reorder = FALSE
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+        cluster_column_slices = FALSE
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         row_km = 1
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         column_km = 1
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         if(verbose) qqcat("matrix is character. Do not cluster unless distance method is provided.\n")
... ...
@@ -503,7 +503,7 @@ setMethod(f = "draw",
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     }
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     layout = grid.layout(nrow = length(HEATMAP_LIST_LAYOUT_COLUMN_COMPONENT), 
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-        ncol = length(HEATMAP_LAYOUT_ROW_COMPONENT), 
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+        ncol = length(HEATMAP_LIST_LAYOUT_ROW_COMPONENT), 
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         widths = component_width(object), 
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         heights = component_height(object))
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@@ -377,7 +377,6 @@ setMethod(f = "annotation_legend_size",
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 })
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379 379
 # create a viewport which contains legend
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-# currently, one-row or one-column legend is supported
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 draw_legend = function(ColorMappingList, ColorMappingParamList, side = c("right", "left", "top", "bottom"), 
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     plot = TRUE, gap = unit(2, "mm"), legend_list = list(), padding = unit(c(0, 0, 0, 0), "mm"), 
383 382
     max_height = unit(dev.size("cm")[2], "cm"), max_width = unit(dev.size("cm")[1], "cm"), ...) {
... ...
@@ -398,7 +397,7 @@ draw_legend = function(ColorMappingList, ColorMappingParamList, side = c("right"
398 397
         if(side %in% c("left", "right")) {
399 398
             pk = packLegend(list = cm_grob, gap = gap, direction = "vertical", max_height = max_height)  
400 399
         } else {
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-            pk = packLegend(list = cm_grob, gap = gap, direction = "horizontal", max_width = max_width)
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+            pk = packLegend(list = cm_grob, gap = unit(4, "mm"), direction = "horizontal", max_width = max_width)
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         }
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     }
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@@ -15,4 +15,5 @@ method and the \code{\%v\%v} method so that above three classes can be appended
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -22,4 +22,5 @@ See \code{\link{AnnotationFunction}} constructor for details.
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -40,4 +40,5 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -196,4 +196,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -25,4 +25,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -80,4 +80,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -40,4 +40,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -1,5 +1,6 @@
1 1
 \name{adjust_heatmap_list-HeatmapList-method}
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 \alias{adjust_heatmap_list,HeatmapList-method}
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+\alias{adjust_heatmap_list}
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 \title{
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 Adjust Heatmap List
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 }
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@@ -23,8 +24,8 @@ This function is only for internal use.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
25 26
 }
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-\alias{adjust_heatmap_list}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -20,4 +20,5 @@ anno_link(...)
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -1,5 +1,6 @@
1 1
 \name{annotation_legend_size-HeatmapList-method}
2 2
 \alias{annotation_legend_size,HeatmapList-method}
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+\alias{annotation_legend_size}
3 4
 \title{
4 5
 Size of the Annotation Legends
5 6
 }
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@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
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-\alias{annotation_legend_size}
31 31
 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -1,5 +1,6 @@
1 1
 \name{color_mapping_legend-ColorMapping-method}
2 2
 \alias{color_mapping_legend,ColorMapping-method}
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+\alias{color_mapping_legend}
3 4
 \title{
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 Draw Legend Based on Color Mapping
5 6
 }
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@@ -65,8 +66,8 @@ A \code{\link{Legends-class}} object.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
67 68
 }
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-\alias{color_mapping_legend}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -31,4 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -24,4 +24,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -26,4 +26,5 @@ The environment is at \code{object@var_env}.
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -21,4 +21,5 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -17,4 +17,5 @@ default_get_type(x)
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -17,4 +17,5 @@ dend_heights(x)
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -28,4 +28,5 @@ A \code{\link{grob}} object which is contructed by \code{\link[grid:grid.segment
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -17,4 +17,5 @@ Dimension of the Heatmap
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -28,4 +28,5 @@ which is generally for testing purpose.
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -175,4 +175,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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 }
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@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation-Heatmap-method}
2 2
 \alias{draw_annotation,Heatmap-method}
3
+\alias{draw_annotation}
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 \title{
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 Draw Heatmap Annotations on the Heatmap
5 6
 }
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@@ -30,8 +31,8 @@ This function returns no value.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
32 33
 }
33
-\alias{draw_annotation}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation_legend-HeatmapList-method}
2 2
 \alias{draw_annotation_legend,HeatmapList-method}
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+\alias{draw_annotation_legend}
3 4
 \title{
4 5
 Draw legends for All Annotations
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 }
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@@ -31,8 +32,8 @@ This function returns no value.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{draw_annotation_legend}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -1,5 +1,6 @@
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 \name{draw_dend-Heatmap-method}
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 \alias{draw_dend,Heatmap-method}
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+\alias{draw_dend}
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 \title{
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 Draw Heatmap Dendrograms
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 }
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@@ -33,8 +34,8 @@ This function returns no value.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{draw_dend}
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 \examples{
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 # There is no example
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 NULL
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 }
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@@ -1,5 +1,6 @@
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 \name{draw_dimnames-Heatmap-method}
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 \alias{draw_dimnames,Heatmap-method}
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+\alias{draw_dimnames}
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 \title{
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 Draw row names or column names
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 }
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@@ -29,8 +30,8 @@ This function returns no value.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{draw_dimnames}
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 \examples{
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 # There is no example
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 }
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@@ -1,5 +1,6 @@
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 \name{draw_heatmap_body-Heatmap-method}
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 \alias{draw_heatmap_body,Heatmap-method}
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+\alias{draw_heatmap_body}
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 \title{
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 Draw Heatmap Body
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 }
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@@ -28,8 +29,8 @@ This function returns no value.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{draw_heatmap_body}
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 \examples{
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 # There is no example
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 NULL
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 }
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@@ -1,5 +1,6 @@
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 \name{draw_heatmap_legend-HeatmapList-method}
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 \alias{draw_heatmap_legend,HeatmapList-method}
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+\alias{draw_heatmap_legend}
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 \title{
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 Draw legends for All Heatmaps
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 }
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@@ -32,8 +33,8 @@ This function returns no value.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{draw_heatmap_legend}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -1,5 +1,6 @@
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 \name{draw_heatmap_list-HeatmapList-method}
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 \alias{draw_heatmap_list,HeatmapList-method}
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+\alias{draw_heatmap_list}
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 \title{
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 Draw the List of Heatmaps
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 }
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@@ -25,8 +26,8 @@ This function returns no value.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{draw_heatmap_list}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -32,4 +32,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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 }
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@@ -1,5 +1,6 @@
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 \name{get_color_mapping_list-HeatmapAnnotation-method}
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 \alias{get_color_mapping_list,HeatmapAnnotation-method}
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+\alias{get_color_mapping_list}
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 \title{
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 Get a List of ColorMapping objects
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 }
... ...
@@ -25,8 +26,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{get_color_mapping_list}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -1,5 +1,6 @@
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 \name{get_legend_param_list-HeatmapAnnotation-method}
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 \alias{get_legend_param_list,HeatmapAnnotation-method}
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+\alias{get_legend_param_list}
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 \title{
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 Get a List of Annotation Legend Parameters
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 }
... ...
@@ -25,8 +26,8 @@ A list.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{get_legend_param_list}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -1,5 +1,6 @@
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 \name{heatmap_legend_size-HeatmapList-method}
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 \alias{heatmap_legend_size,HeatmapList-method}
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+\alias{heatmap_legend_size}
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 \title{
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 Size of the Heatmap Legends
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 }
... ...
@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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 }
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-\alias{heatmap_legend_size}
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -18,4 +18,5 @@ Height of the Heatmap
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 \examples{
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 # There is no example
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 NULL
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 }
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@@ -21,4 +21,5 @@ Internally used.
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 \examples{
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 # There is no example
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 NULL
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 }
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@@ -18,4 +18,5 @@ Height of the Heatmap List
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 \examples{
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 # There is no example
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 NULL
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 }
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@@ -21,4 +21,5 @@ Internally used.
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 \examples{
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 # There is no example
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 }
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@@ -23,4 +23,5 @@ Internally used.
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 \examples{
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 # There is no example
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 }
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@@ -23,4 +23,5 @@ Internally used.
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 \examples{
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 # There is no example
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 }
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@@ -23,4 +23,5 @@ Internally used.
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 \examples{
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 # There is no example
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 }
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@@ -20,4 +20,5 @@ The physical height of the grob can be get by \code{convertWidth(grobHeight(axis
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 \examples{
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 # There is no example
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 NULL
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+
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 }
... ...
@@ -17,4 +17,5 @@ Grob height for packed_legends
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 \examples{
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 # There is no example
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 NULL
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+
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 }
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@@ -17,4 +17,5 @@ Grob height for legend_body
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 \examples{
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 # There is no example
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 NULL
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+
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 }
... ...
@@ -17,4 +17,5 @@ Grob height for packed_legends
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 \examples{
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 # There is no example
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 NULL
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+
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 }
... ...
@@ -25,4 +25,5 @@ will also be sychronized in \code{\link{ht_opt}}.
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 \examples{
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 # There is no example
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 NULL
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+
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 }
... ...
@@ -17,4 +17,5 @@ Number of Annotations
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 \examples{
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 # There is no example
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 NULL
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+
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 }
... ...
@@ -17,4 +17,5 @@ Length of the HeatmapList object
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 \examples{
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 # There is no example
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 NULL
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+
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 }
... ...
@@ -15,4 +15,5 @@ A vector of viewport names.
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 \examples{
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 # There is no example
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 NULL
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+
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 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{make_column_cluster-Heatmap-method}
2 2
 \alias{make_column_cluster,Heatmap-method}
3
+\alias{make_column_cluster}
3 4
 \title{
4 5
 Make Cluster on Columns
5 6
 }
... ...
@@ -28,8 +29,8 @@ A \code{\link{Heatmap-class}} object.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{make_column_cluster}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
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+
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 }
... ...
@@ -32,4 +32,5 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -130,4 +130,5 @@ Zuguang Gu <z.gu@dkfz.de>
130 130
 \examples{
131 131
 # There is no example
132 132
 NULL
133
+
133 134
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{make_row_cluster-Heatmap-method}
2 2
 \alias{make_row_cluster,Heatmap-method}
3
+\alias{make_row_cluster}
3 4
 \title{
4 5
 Make Cluster on Rows
5 6
 }
... ...
@@ -27,8 +28,8 @@ A \code{\link{Heatmap-class}} object.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{make_row_cluster}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{map_to_colors-ColorMapping-method}
2 2
 \alias{map_to_colors,ColorMapping-method}
3
+\alias{map_to_colors}
3 4
 \title{
4 5
 Map Values to Colors
5 6
 }
... ...
@@ -34,4 +35,3 @@ col_fun = colorRamp2(c(0, 1), c("white", "red"))
34 35
 cm = ColorMapping(col_fun = col_fun)
35 36
 map_to_colors(cm, runif(10))
36 37
 }
37
-\alias{map_to_colors}
... ...
@@ -17,4 +17,5 @@ Names of the heatmaps/annotations
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Number of Columns in the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -22,4 +22,5 @@ it returns \code{NA}.
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
+
25 26
 }
... ...
@@ -21,4 +21,5 @@ It returns the \code{n} slot of the annotaton function. If it does not exist, it
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -22,4 +22,5 @@ The sets (by \code{\link{set_name}}) from all combination matrice should be the
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
+
25 26
 }
... ...
@@ -17,4 +17,5 @@ Number of Rows in the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -90,4 +90,5 @@ Zuguang Gu <z.gu@dkfz.de>
90 90
 \examples{
91 91
 # There is no example
92 92
 NULL
93
+
93 94
 }
... ...
@@ -23,4 +23,5 @@ by the combination matrix.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -39,4 +39,5 @@ Zuguang Gu <z.gu@dkfz.de>
39 39
 \examples{
40 40
 # There is no example
41 41
 NULL
42
+
42 43
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{prepare-Heatmap-method}
2 2
 \alias{prepare,Heatmap-method}
3
+\alias{prepare}
3 4
 \title{
4 5
 Prepare the Heatmap
5 6
 }
... ...
@@ -33,8 +34,8 @@ The \code{\link{Heatmap-class}} object.
33 34
 \author{
34 35
 Zuguang Gu <z.gu@dkfz.de>
35 36
 }
36
-\alias{prepare}
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
+
40 41
 }
... ...
@@ -18,4 +18,5 @@ Print the comb_mat Object
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{re_size-HeatmapAnnotation-method}
2 2
 \alias{re_size,HeatmapAnnotation-method}
3
+\alias{re_size}
3 4
 \title{
4 5
 Resize the Width or Height of Heatmap Annotations
5 6
 }
... ...
@@ -41,8 +42,8 @@ The basic rules are (take \code{height} and \code{annotation_height} for example
41 42
      and \code{anno_simple_size} is disabled.
42 43
 6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.
43 44
 }
44
-\alias{re_size}
45 45
 \examples{
46 46
 # There is no example
47 47
 NULL
48
+
48 49
 }
... ...
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_barplot}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_boxplot}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_density}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_histogram}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_link}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_points}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_text}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{set_component_height-Heatmap-method}
2 2
 \alias{set_component_height,Heatmap-method}
3
+\alias{set_component_height}
3 4
 \title{
4 5
 Set Height of Heatmap Component
5 6
 }
... ...
@@ -29,8 +30,8 @@ The \code{\link{Heatmap-class}} object.
29 30
 \author{
30 31
 Zuguang Gu <z.gu@dkfz.de>
31 32
 }
32
-\alias{set_component_height}
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{set_component_width-Heatmap-method}
2 2
 \alias{set_component_width,Heatmap-method}
3
+\alias{set_component_width}
3 4
 \title{
4 5
 Set Width of Heatmap Component
5 6
 }
... ...
@@ -28,8 +29,8 @@ The \code{\link{Heatmap-class}} object.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{set_component_width}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -17,4 +17,5 @@ Print the AnnotationFunction Object
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -24,4 +24,5 @@ This function returns no value.
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -25,4 +25,5 @@ Internally used.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ Internally used.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -21,4 +21,5 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -21,4 +21,5 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Print the Summary of a Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ Summary of a Heatmap List
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -37,4 +37,5 @@ how to set the right annotation or left annotation in \code{\link{UpSet}}, pleas
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
+
40 41
 }
... ...
@@ -37,4 +37,5 @@ how to set the top annotation or bottom annotation in \code{\link{UpSet}}, pleas
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
+
40 41
 }
... ...
@@ -18,4 +18,5 @@ Width of the Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Width of the Heatmap List
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -20,4 +20,5 @@ The physical width of the grob can be get by \code{convertWidth(grobWidth(axis_g
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -17,4 +17,5 @@ Grob width for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob width for legend_body
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob width for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }