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Zuguang Gu authored on 12/10/2018 19:19:48
Showing146 changed files

... ...
@@ -10,7 +10,7 @@ Imports: circlize (>= 0.4.1), GetoptLong, colorspace,
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     RColorBrewer, GlobalOptions (>= 0.1.0)
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 Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust, 
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     dendsort, HilbertCurve, Cairo, png, jpeg, tiff, fastcluster,
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-    dendextend (>= 1.0.1), grImport, grImport2, rsvg
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+    dendextend (>= 1.0.1), grImport, grImport2, rsvg, glue
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 VignetteBuilder: knitr
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 Description: Complex heatmaps are efficient to visualize associations 
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     between different sources of data sets and reveal potential structures. 
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@@ -1,31 +1,31 @@
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-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
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-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
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-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
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 setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
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-setGeneric('draw', function(object, ...) standardGeneric('draw'))
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-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
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-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
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+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
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+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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 setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
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+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
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+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
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+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
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 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
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+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
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+setGeneric('resize', function(object, ...) standardGeneric('resize'))
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+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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 setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
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+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
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+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
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+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
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+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
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+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
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+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
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+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
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 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
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-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
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-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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 setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
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 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
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-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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+setGeneric('draw', function(object, ...) standardGeneric('draw'))
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 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
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-setGeneric('resize', function(object, ...) standardGeneric('resize'))
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-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
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-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
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-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
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-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
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-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
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-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
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-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
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-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
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-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
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-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
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 setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
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+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
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+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
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+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
... ...
@@ -97,8 +97,8 @@ anno_width_and_height = function(which, width = NULL, height = NULL,
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 # -show_name It is used to turn off the drawing of annotation names in `HeatmapAnnotation`. Annotations always have names
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 #        associated and normally they will be drawn beside the annotation graphics to tell what the annotation is about.
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 #        e.g. the annotation names put beside the points annotation graphics. However, for some of the annotations, the names
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-#        are not necessarily to be drawn, such as text annotations drawn by `anno_text` or an empty annotation drawn by `anno_empty()`.
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-#        In this case, when `show_names` is set to `FALSE`, there will be no annotation names drawn for the annotation.
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+#        are not necessarily to be drawn, such as text annotations drawn by `anno_text` or an empty annotation drawn by `anno_empty`.
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+#        In this case, when ``show_names`` is set to ``FALSE``, there will be no annotation names drawn for the annotation.
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 # -width The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation,
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 #        the width must be an absolute unit. Since the ``AnnotationFunction`` object is always contained by the `SingleAnnotation-class`object,
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 #        you can only set the width of row annotations or height of column annotations, while e.g. the height of the row annotation is always ``unit(1, "npc")``
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@@ -348,6 +348,9 @@ setMethod(f = "draw",
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 	if(test2) {
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         grid.newpage()
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         pushViewport(viewport(width = 0.8, height = 0.8))
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+        if(is.na(object@n)) {
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+        	object@n = 1
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+        }
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     }
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     verbose = ht_opt$verbose
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@@ -1,3 +1,4 @@
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+# -anno_simple_size size of the simple annotation.# -anno_simple_size size of the simple annotation.# -anno_simple_size size of the simple annotation.
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 # == title
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 # Empty Annotation
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@@ -110,6 +111,7 @@ subset_vector = function(x, i) x[i]
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 #          the value of ``pt_size`` can be a vector, while if ``x`` is a matrix, ``pt_size`` can
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 #          only be a single value.
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 # -pt_gp Graphic parameters for points/symbols. The length setting is same as ``pt_size``.
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+# -anno_simple_size size of the simple annotation.
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 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.
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 # -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.
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 #
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@@ -170,7 +170,7 @@ setMethod(f = "add_heatmap",
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 #
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 # == param
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 # -object a `HeatmapList-class` object.
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-# -newpage whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use `grid::grabExpr`.
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+# -newpage whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use `grid::grid.grabExpr`.
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 # -row_title title on the row.
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 # -row_title_side will the title be put on the left or right of the heatmap.
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 # -row_title_gp graphic parameters for drawing text.
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@@ -190,7 +190,8 @@ setMethod(f = "add_heatmap",
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 # -ht_gap same as ``gap``.
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 # -main_heatmap index of main heatmap. The value can be a numeric index or the heatmap name
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 # -padding padding of the whole plot. The value is a unit vector of length 4, which corresponds to bottom, left, top and right.
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-# -adjust_annotation_name whether take annotation name into account when calculating positions of graphic elements.
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+# -adjust_annotation_extension whether take annotation name into account when calculating positions of graphic elements.
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+# -auto_adjust whether auto adjust
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 # -row_dend_side side of the dendrogram from the main heatmap
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 # -row_sub_title_side side of the row title from the main heatmap
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 # -column_dend_side side of the dendrogram from the main heatmap
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@@ -208,7 +209,8 @@ setMethod(f = "add_heatmap",
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 # -split this modifies ``split`` of the main heatmap
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 # -row_km this modifies ``row_km`` of the main heatmap
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 # -row_split this modifies ``row_split`` of the main heatmap
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-# -heatmap_body_height this modifies ``heatmap_body_height`` of the main heatmap
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+# -height this modifies ``height`` of the main heatmap
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+# -heatmap_height this modifies ``heatmap_height`` of the main heatmap
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 # -column_gap this modifies ``column_gap`` of the main heatmap
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 # -cluster_columns this modifies ``cluster_columns`` of the main heatmap
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 # -clustering_distance_columns this modifies ``clustering_distance_columns`` of the main heatmap
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@@ -220,7 +222,8 @@ setMethod(f = "add_heatmap",
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 # -column_order this modifies ``column_order`` of the main heatmap
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 # -column_km this modifies ``column_km`` of the main heatmap
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 # -column_split this modifies ``column_split`` of the main heatmap
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-# -heatmap_body_width this set the value in `ht_opt` and reset back after the plot is done
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+# -width this modifies ``width`` of the main heatmap
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+# -heatmap_width this modifies ``heatmap_width`` of the main heatmap
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 # -heatmap_row_names_gp  this set the value in `ht_opt` and reset back after the plot is done
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 # -heatmap_column_names_gp this set the value in `ht_opt` and reset back after the plot is done
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 # -heatmap_row_title_gp this set the value in `ht_opt` and reset back after the plot is done
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@@ -20,6 +20,7 @@
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 # -ht_gap gap between heatmaps, should be a `grid::unit` object.
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 # -main_heatmap name or index for the main heatmap
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 # -padding padding of the plot
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+# -auto_adjust whether autoadjust
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 # -row_dend_side if auto adjust, where to put the row dendrograms for the main heatmap
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 # -row_sub_title_side row sub title
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 # -column_dend_side column dend
... ...
@@ -140,7 +141,7 @@ setMethod(f = "make_layout",
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         grid::upViewport()
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         object@layout$page_size = unit.c(convertWidth(unit(1, "npc"), "mm"),
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                                          convertHeight(unit(1, "npc"), "mm"))
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-        grid::downViewport()
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+        grid::downViewport(current_vp)
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     }
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     object@ht_list_param$padding = padding
... ...
@@ -283,7 +284,7 @@ setMethod(f = "make_layout",
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             if(row_dend_width[[1]] == 0) {
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                 object@ht_list[[i_main]]@row_dend_param$width = unit(0, "mm")
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             } else {
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-                object@ht_list[[i_main]]@row_dend_param$width = row_dend_width + DENDROGRAM_PADDING  # append the gap
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+                object@ht_list[[i_main]]@row_dend_param$width = row_dend_width + ht_opt$DENDROGRAM_PADDING  # append the gap
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             }
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         }
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         if(!is.null(show_row_dend)) {
... ...
@@ -402,7 +403,7 @@ setMethod(f = "make_layout",
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             if(column_dend_width[[1]] == 0) {
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                 object@ht_list[[i_main]]@column_dend_param$width = unit(0, "mm")
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             } else {
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-                object@ht_list[[i_main]]@column_dend_param$width = column_dend_width + DENDROGRAM_PADDING  # append the gap
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+                object@ht_list[[i_main]]@column_dend_param$width = column_dend_width + ht_opt$DENDROGRAM_PADDING  # append the gap
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             }
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         }
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         if(!is.null(show_column_dend)) {
... ...
@@ -73,6 +73,7 @@ SingleAnnotation = setClass("SingleAnnotation",
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 # -name_offset Offset to the annotation, a `grid::unit` object.
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 # -name_side 'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations
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 # -name_rot Rotation of the annotation name, it can only take values in ``c(0, 90, 180, 270)``.
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+# -anno_simple_size size of the simple annotation.
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 # -width The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation,
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 #        the width must be an absolute unit.
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 # -height The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation,
... ...
@@ -22,7 +22,7 @@
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 # -heatmap_column_names_gp set ``column_names_gp`` in all `Heatmap`.
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 # -heatmap_row_title_gp set ``row_title_gp`` in all `Heatmap`.
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 # -heatmap_column_title_gp set ``column_title_gp`` in all `Heatmap`.
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-# -heatmap_border set `border` in all `Heatmap`.
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+# -heatmap_border set ``border`` in all `Heatmap`.
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 #
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 # Following parameters to control the legends: 
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 #
... ...
@@ -734,6 +734,8 @@ horizontal_continuous_legend_body = function(at, labels = at, col_fun,
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 # == param
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 # -... A list of objects returned by `Legend`.
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 # -gap Gap between two neighbouring legends. The value is a `grid::unit` object with length of one.
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+# -row_gap Horizontal gaps between legends.
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+# -column_gap Vertical gaps between legends.
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 # -direction The direction to arrange legends.
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 # -max_width The maximal width of the total packed legends. It only works for horizontal arrangement.
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 #           If the total width of the legends exceeds it, the legends will be arranged into several rows.
... ...
@@ -290,7 +290,7 @@ rep.list = function(x, n) {
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 # A vector of viewport names.
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 #
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 list_component = function() {
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-    vp = grid.ls(viewports = TRUE, grob = FALSE, flatten = FALSE, print = FALSE)
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+    vp = grid.ls(viewports = TRUE, grobs = FALSE, flatten = FALSE, print = FALSE)
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     vp = unlist(vp)
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     attributes(vp) = NULL
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     vp = vp[!grepl("^\\d+$", vp)]
... ...
@@ -15,4 +15,5 @@ method so that above three classes can be appended to each other.
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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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@@ -23,4 +23,5 @@ 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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@@ -21,7 +21,7 @@ AnnotationFunction(fun, fun_name = "", which = c("column", "row"),
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   \item{data_scale}{The data scale on the data axis (y-axis for column annotation and x-axis for row annotation). It is only used when \code{\link{decorate_annotation}} is used with "native" unit coordinates.}
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   \item{subset_rule}{The rule of subsetting variables in \code{var_import}. It should be set when users want the final object to be subsetable. See **Details** section.}
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   \item{subsetable}{Whether the object is subsetable?}
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-  \item{show_name}{It is used to turn off the drawing of annotation names in \code{\link{HeatmapAnnotation}}. Annotations always have names associated and normally they will be drawn beside the annotation graphics to tell what the annotation is about. e.g. the annotation names put beside the points annotation graphics. However, for some of the annotations, the names are not necessarily to be drawn, such as text annotations drawn by \code{\link{anno_text}} or an empty annotation drawn by \code{\link{anno_empty()}}. In this case, when \code{\link{show_names}} is set to \code{\link{FALSE}}, there will be no annotation names drawn for the annotation.}
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+  \item{show_name}{It is used to turn off the drawing of annotation names in \code{\link{HeatmapAnnotation}}. Annotations always have names associated and normally they will be drawn beside the annotation graphics to tell what the annotation is about. e.g. the annotation names put beside the points annotation graphics. However, for some of the annotations, the names are not necessarily to be drawn, such as text annotations drawn by \code{\link{anno_text}} or an empty annotation drawn by \code{\link{anno_empty}}. In this case, when \code{show_names} is set to \code{FALSE}, there will be no annotation names drawn for the annotation.}
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   \item{width}{The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation, the width must be an absolute unit. Since the \code{AnnotationFunction} object is always contained by the \code{\link{SingleAnnotation-class}}object, you can only set the width of row annotations or height of column annotations, while e.g. the height of the row annotation is always \code{unit(1, "npc")} which means it always fully filled in the parent \code{SingleAnnotation} and only in \code{\link{SingleAnnotation}} or even \code{\link{HeatmapAnnotation}} can adjust the height of the row annotations.}
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   \item{height}{The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit.}
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... ...
@@ -121,4 +121,5 @@ ComplexHeatmap Complete Reference ().
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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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@@ -36,4 +36,5 @@ You can refer to the ComplexHeatmap Complete Reference for all the information o
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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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@@ -23,4 +23,5 @@ If the heatmap list is horizontal, \code{i} is the real row indices and \code{j}
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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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@@ -185,4 +185,5 @@ 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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 }
... ...
@@ -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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@@ -74,4 +74,5 @@ 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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@@ -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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 }
... ...
@@ -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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 }
... ...
@@ -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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 }
... ...
@@ -39,6 +39,7 @@ SingleAnnotation(name, value, col, fun,
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   \item{name_offset}{Offset to the annotation, a \code{\link[grid]{unit}} object.}
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   \item{name_side}{'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations}
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   \item{name_rot}{Rotation of the annotation name, it can only take values in \code{c(0, 90, 180, 270)}.}
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+  \item{anno_simple_size}{size of the simple annotation.}
42 43
   \item{width}{The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation, the width must be an absolute unit.}
43 44
   \item{height}{The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit.}
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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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 }
... ...
@@ -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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 }
... ...
@@ -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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 }
... ...
@@ -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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 }
... ...
@@ -11,8 +11,8 @@ Method dispatch page for \code{add_heatmap}.
11 11
 
12 12
 \itemize{
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 \item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
14
-\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 14
 \item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
15
+\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method
16 16
 }
17 17
 }
18 18
 \examples{
... ...
@@ -1,5 +1,6 @@
1 1
 \name{adjust_heatmap_list-HeatmapList-method}
2 2
 \alias{adjust_heatmap_list,HeatmapList-method}
3
+\alias{adjust_heatmap_list}
3 4
 \title{
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 Adjust heatmap list
5 6
 }
... ...
@@ -22,8 +23,8 @@ This function is only for internal use.
22 23
 \author{
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 Zuguang Gu <z.gu@dkfz.de>
24 25
 }
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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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 }
... ...
@@ -20,4 +20,5 @@ anno_link(...)
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 \examples{
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 # There is no example
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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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 }
... ...
@@ -24,6 +24,7 @@ anno_simple(x, col, na_col = "grey",
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   \item{pch}{Points/symbols that are added on top of the annotation grids. The value can be numeric or single letters. It can be a vector if \code{x} is a vector and a matrix if \code{x} is a matrix. No points are drawn if the corresponding values are NA.}
25 25
   \item{pt_size}{Size of the points/symbols. It should be a \code{\link[grid]{unit}} object. If \code{x} is a vector, the value of \code{pt_size} can be a vector, while if \code{x} is a matrix, \code{pt_size} can only be a single value.}
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   \item{pt_gp}{Graphic parameters for points/symbols. The length setting is same as \code{pt_size}.}
27
+  \item{anno_simple_size}{size of the simple annotation.}
27 28
   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
28 29
   \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
29 30
 
... ...
@@ -26,4 +26,5 @@ A \code{\link[grid]{grob}} object.
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{annotation_legend_size-HeatmapList-method}
2 2
 \alias{annotation_legend_size,HeatmapList-method}
3
+\alias{annotation_legend_size}
3 4
 \title{
4 5
 Size of the annotation legend viewport
5 6
 }
... ...
@@ -28,8 +29,8 @@ A \code{\link[grid]{unit}} object.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{annotation_legend_size}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{color_mapping_legend-ColorMapping-method}
2 2
 \alias{color_mapping_legend,ColorMapping-method}
3
+\alias{color_mapping_legend}
3 4
 \title{
4 5
 Draw Legend Based on Color Mapping
5 6
 }
... ...
@@ -65,8 +66,8 @@ A \code{\link{Legends-class}} object.
65 66
 \author{
66 67
 Zuguang Gu <z.gu@dkfz.de>
67 68
 }
68
-\alias{color_mapping_legend}
69 69
 \examples{
70 70
 # There is no example
71 71
 NULL
72
+
72 73
 }
... ...
@@ -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
 }
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{column_order}.
10 10
 \code{column_order} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14 13
 \item \code{\link{column_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
14
+\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -31,4 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -24,4 +24,5 @@ Zuguang Gu <z.gu@dkfz.de>
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}.
10 10
 \code{component_height} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14 13
 \item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
14
+\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
+
33 34
 }
... ...
@@ -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
 }
... ...
@@ -26,4 +26,5 @@ The environment is at \code{object@var_env}.
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -21,4 +21,5 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{copy_all}.
10 10
 \code{copy_all} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
14 13
 \item \code{\link{copy_all,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
14
+\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -17,4 +17,5 @@ dend_heights(x)
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -28,4 +28,5 @@ A \code{\link{grob}} object which is generally contructed by \code{\link[grid]{s
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -17,4 +17,5 @@ Dimension of the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -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
 }
... ...
@@ -27,4 +27,5 @@ which is generally for testing purpose.
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -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
 }
... ...
@@ -89,7 +89,7 @@ Draw a list of heatmaps
89 89
 \arguments{
90 90
 
91 91
   \item{object}{a \code{\link{HeatmapList-class}} object.}
92
-  \item{newpage}{whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use \code{\link[grid]{grabExpr}}.}
92
+  \item{newpage}{whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use \code{\link[grid]{grid.grabExpr}}.}
93 93
   \item{row_title}{title on the row.}
94 94
   \item{row_title_side}{will the title be put on the left or right of the heatmap.}
95 95
   \item{row_title_gp}{graphic parameters for drawing text.}
... ...
@@ -109,7 +109,8 @@ Draw a list of heatmaps
109 109
   \item{ht_gap}{same as \code{gap}.}
110 110
   \item{main_heatmap}{index of main heatmap. The value can be a numeric index or the heatmap name}
111 111
   \item{padding}{padding of the whole plot. The value is a unit vector of length 4, which corresponds to bottom, left, top and right.}
112
-  \item{adjust_annotation_name}{whether take annotation name into account when calculating positions of graphic elements.}
112
+  \item{adjust_annotation_extension}{whether take annotation name into account when calculating positions of graphic elements.}
113
+  \item{auto_adjust}{whether auto adjust}
113 114
   \item{row_dend_side}{side of the dendrogram from the main heatmap}
114 115
   \item{row_sub_title_side}{side of the row title from the main heatmap}
115 116
   \item{column_dend_side}{side of the dendrogram from the main heatmap}
... ...
@@ -127,7 +128,8 @@ Draw a list of heatmaps
127 128
   \item{split}{this modifies \code{split} of the main heatmap}
128 129
   \item{row_km}{this modifies \code{row_km} of the main heatmap}
129 130
   \item{row_split}{this modifies \code{row_split} of the main heatmap}
130
-  \item{heatmap_body_height}{this modifies \code{heatmap_body_height} of the main heatmap}
131
+  \item{height}{this modifies \code{height} of the main heatmap}
132
+  \item{heatmap_height}{this modifies \code{heatmap_height} of the main heatmap}
131 133
   \item{column_gap}{this modifies \code{column_gap} of the main heatmap}
132 134
   \item{cluster_columns}{this modifies \code{cluster_columns} of the main heatmap}
133 135
   \item{clustering_distance_columns}{this modifies \code{clustering_distance_columns} of the main heatmap}
... ...
@@ -139,7 +141,8 @@ Draw a list of heatmaps
139 141
   \item{column_order}{this modifies \code{column_order} of the main heatmap}
140 142
   \item{column_km}{this modifies \code{column_km} of the main heatmap}
141 143
   \item{column_split}{this modifies \code{column_split} of the main heatmap}
142
-  \item{heatmap_body_width}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}
144
+  \item{width}{this modifies \code{width} of the main heatmap}
145
+  \item{heatmap_width}{this modifies \code{heatmap_width} of the main heatmap}
143 146
   \item{heatmap_row_names_gp}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}
144 147
   \item{heatmap_column_names_gp}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}
145 148
   \item{heatmap_row_title_gp}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}
... ...
@@ -171,4 +174,5 @@ Zuguang Gu <z.gu@dkfz.de>
171 174
 \examples{
172 175
 # There is no example
173 176
 NULL
177
+
174 178
 }
... ...
@@ -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
 }
... ...
@@ -11,11 +11,11 @@ Method dispatch page for \code{draw}.
11 11
 
12 12
 \itemize{
13 13
 \item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
14
-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
15
-\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
14
+\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method
16 15
 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
16
+\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
17
+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
17 18
 \item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
18
-\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method
19 19
 }
20 20
 }
21 21
 \examples{
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation-Heatmap-method}
2 2
 \alias{draw_annotation,Heatmap-method}
3
+\alias{draw_annotation}
3 4
 \title{
4 5
 Draw Heatmap Annotations on the Heatmap
5 6
 }
... ...
@@ -30,8 +31,8 @@ This function returns no value.
30 31
 \author{
31 32
 Zuguang Gu <z.gu@dkfz.de>
32 33
 }
33
-\alias{draw_annotation}
34 34
 \examples{
35 35
 # There is no example
36 36
 NULL
37
+
37 38
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation_legend-HeatmapList-method}
2 2
 \alias{draw_annotation_legend,HeatmapList-method}
3
+\alias{draw_annotation_legend}
3 4
 \title{
4 5
 Draw legends for all column annotations
5 6
 }
... ...
@@ -27,8 +28,8 @@ This function returns no value.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{draw_annotation_legend}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_dend-Heatmap-method}
2 2
 \alias{draw_dend,Heatmap-method}
3
+\alias{draw_dend}
3 4
 \title{
4 5
 Draw Heatmap Dendrograms
5 6
 }
... ...
@@ -33,8 +34,8 @@ This function returns no value.
33 34
 \author{
34 35
 Zuguang Gu <z.gu@dkfz.de>
35 36
 }
36
-\alias{draw_dend}
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
+
40 41
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_dimnames-Heatmap-method}
2 2
 \alias{draw_dimnames,Heatmap-method}
3
+\alias{draw_dimnames}
3 4
 \title{
4 5
 Draw row names or column names
5 6
 }
... ...
@@ -29,8 +30,8 @@ This function returns no value.
29 30
 \author{
30 31
 Zuguang Gu <z.gu@dkfz.de>
31 32
 }
32
-\alias{draw_dimnames}
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_body-Heatmap-method}
2 2
 \alias{draw_heatmap_body,Heatmap-method}
3
+\alias{draw_heatmap_body}
3 4
 \title{
4 5
 Draw the Heatmap Body
5 6
 }
... ...
@@ -28,8 +29,8 @@ This function returns no value.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{draw_heatmap_body}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_legend-HeatmapList-method}
2 2
 \alias{draw_heatmap_legend,HeatmapList-method}
3
+\alias{draw_heatmap_legend}
3 4
 \title{
4 5
 Draw legends for all heatmaps
5 6
 }
... ...
@@ -27,8 +28,8 @@ This function returns no value.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{draw_heatmap_legend}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_list-HeatmapList-method}
2 2
 \alias{draw_heatmap_list,HeatmapList-method}
3
+\alias{draw_heatmap_list}
3 4
 \title{
4 5
 Draw the list of heatmaps
5 6
 }
... ...
@@ -25,8 +26,8 @@ This function returns no value.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{draw_heatmap_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -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
 }
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
+
33 34
 }
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{draw_title}.
10 10
 \code{draw_title} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{draw_title,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14 13
 \item \code{\link{draw_title,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
14
+\item \code{\link{draw_title,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -1,5 +1,6 @@
1 1
 \name{get_color_mapping_list-HeatmapAnnotation-method}
2 2
 \alias{get_color_mapping_list,HeatmapAnnotation-method}
3
+\alias{get_color_mapping_list}
3 4
 \title{
4 5
 Get a List of ColorMapping objects
5 6
 }
... ...
@@ -25,8 +26,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{get_color_mapping_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{get_legend_param_list-HeatmapAnnotation-method}
2 2
 \alias{get_legend_param_list,HeatmapAnnotation-method}
3
+\alias{get_legend_param_list}
3 4
 \title{
4 5
 Get a List of Annotation Legend Parameters
5 6
 }
... ...
@@ -25,8 +26,8 @@ A list.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{get_legend_param_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -29,4 +29,5 @@ All the values are measured with \code{native} coordinate.
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -22,4 +22,5 @@ general method. It applies \code{\link[grid]{grid.draw}} on the \code{grob} slot
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
+
25 26
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{heatmap_legend_size-HeatmapList-method}
2 2
 \alias{heatmap_legend_size,HeatmapList-method}
3
+\alias{heatmap_legend_size}
3 4
 \title{
4 5
 Size of the heatmap legend viewport
5 6
 }
... ...
@@ -25,8 +26,8 @@ A \code{\link[grid]{unit}} object.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{heatmap_legend_size}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -18,4 +18,5 @@ Height of the HeatmapAnnotation Object
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ The returned unit x is always in \code{mm}.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Height of the SingleAnnotation object
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ height(x, ...)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -20,4 +20,5 @@ Assign the Height to the AnnotationFunction Object
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -20,4 +20,5 @@ Assign the Height to the HeatmapAnnotation Object
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -20,4 +20,5 @@ Assign the Height to the SingleAnnotation Object
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -20,4 +20,5 @@ height(x, ...) <- value
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -17,4 +17,5 @@ Grob width for annotation_axis
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob height for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob height for legend_body
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Grob height for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -25,4 +25,5 @@ will also be sychronized in \code{\link{ht_opt}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -30,7 +30,7 @@ There are following parameters to control all heatmaps:
30 30
   \item{heatmap_column_names_gp}{set \code{column_names_gp} in all \code{\link{Heatmap}}.}
31 31
   \item{heatmap_row_title_gp}{set \code{row_title_gp} in all \code{\link{Heatmap}}.}
32 32
   \item{heatmap_column_title_gp}{set \code{column_title_gp} in all \code{\link{Heatmap}}.}
33
-  \item{heatmap_border}{set \code{\link{border}} in all \code{\link{Heatmap}}.}
33
+  \item{heatmap_border}{set \code{border} in all \code{\link{Heatmap}}.}
34 34
 }
35 35
 
36 36
 Following parameters to control the legends:
... ...
@@ -17,4 +17,5 @@ Number of Annotations
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -17,4 +17,5 @@ Length of the HeatmapList object
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -15,4 +15,5 @@ A vector of viewport names.
15 15
 \examples{
16 16
 # There is no example
17 17
 NULL
18
+
18 19
 }
... ...
@@ -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
35
+
35 36
 }
... ...
@@ -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
 }
... ...
@@ -82,6 +82,7 @@ Make layout for the complete plot
82 82
   \item{ht_gap}{gap between heatmaps, should be a \code{\link[grid]{unit}} object.}
83 83
   \item{main_heatmap}{name or index for the main heatmap}
84 84
   \item{padding}{padding of the plot}
85
+  \item{auto_adjust}{whether autoadjust}
85 86
   \item{row_dend_side}{if auto adjust, where to put the row dendrograms for the main heatmap}
86 87
   \item{row_sub_title_side}{row sub title}
87 88
   \item{column_dend_side}{column dend}
... ...
@@ -132,4 +133,5 @@ Zuguang Gu <z.gu@dkfz.de>
132 133
 \examples{
133 134
 # There is no example
134 135
 NULL
136
+
135 137
 }
... ...
@@ -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
 }
... ...
@@ -18,4 +18,5 @@ Number of Observations
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -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
 }
... ...
@@ -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
 }
... ...
@@ -71,4 +71,5 @@ Zuguang Gu <z.gu@dkfz.de>
71 71
 \examples{
72 72
 # There is no example
73 73
 NULL
74
+
74 75
 }
... ...
@@ -15,6 +15,8 @@ packLegend(...,gap = unit(2, "mm"), row_gap = unit(2, "mm"), column_gap = unit(2
15 15
 
16 16
   \item{...}{A list of objects returned by \code{\link{Legend}}.}
17 17
   \item{gap}{Gap between two neighbouring legends. The value is a \code{\link[grid]{unit}} object with length of one.}
18
+  \item{row_gap}{Horizontal gaps between legends.}
19
+  \item{column_gap}{Vertical gaps between legends.}
18 20
   \item{direction}{The direction to arrange legends.}
19 21
   \item{max_width}{The maximal width of the total packed legends. It only works for horizontal arrangement. If the total width of the legends exceeds it, the legends will be arranged into several rows.}
20 22
   \item{max_height}{Similar as \code{max_width}, but for the vertical arrangment of legends.}
... ...
@@ -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
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{resize-HeatmapAnnotation-method}
2 2
 \alias{resize,HeatmapAnnotation-method}
3
+\alias{resize}
3 4
 \title{
4 5
 Resize the Width or Height of Heatmap Annotations
5 6
 }
... ...
@@ -40,8 +41,8 @@ the basic rule is:
40 41
      and \code{anno_simple_size} is disabled.
41 42
 6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.
42 43
 }
43
-\alias{resize}
44 44
 \examples{
45 45
 # There is no example
46 46
 NULL
47
+
47 48
 }
... ...
@@ -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
 }
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{row_dend}.
10 10
 \code{row_dend} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14 13
 \item \code{\link{row_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
14
+\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -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
 }
... ...
@@ -10,11 +10,11 @@ Method dispatch page for \code{show}.
10 10
 \code{show} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
+\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
13 14
 \item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
14
-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
15
-\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
16 15
 \item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
17
-\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
16
+\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
17
+\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
18 18
 \item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
19 19
 }
20 20
 }
... ...
@@ -21,4 +21,5 @@ It returns the width if it is a row annotation and the height if it is a column
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -21,4 +21,5 @@ It returns the width if it is a row annotation and the height if it is a column
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ size(x, ...)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -23,4 +23,5 @@ It assigns the width if it is a row annotation and the height if it is a column
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -23,4 +23,5 @@ It assigns to the width if it is a row annotation and the height if it is a colu
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -20,4 +20,5 @@ size(x, ...) <- value
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -18,4 +18,5 @@ subset_matrix_by_row(x, i)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ subset_vector(x, i)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -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
 }
... ...
@@ -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
 }
... ...
@@ -18,4 +18,5 @@ Width of the HeatmapAnnotation Object
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ The returned unit x is always in \code{mm}.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Width of the SingleAnnotation Object
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ width(x, ...)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -20,4 +20,5 @@ Assign the Width to the AnnotationFunction Object
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -20,4 +20,5 @@ Assign the Width to the HeatmapAnnotation Object
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -20,4 +20,5 @@ Assign the Width to the SingleAnnotation Object
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -20,4 +20,5 @@ width(x, ...) <- value
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -17,4 +17,5 @@ Grob width for annotation_axis
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
 }
... ...
@@ -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
 }
... ...
@@ -320,7 +320,7 @@ columnAnnotation(
320 320
 	col = anno_col
321 321
 ) %v%
322 322
 Heatmap(mat_expr[1:40, ], name = "epxression", col = expr_col_fun,
323
-		row_km = 2, row_title = "Expression", heatmap_body_height = unit(6, "cm"))
323
+		row_km = 2, row_title = "Expression", heatmap_height = unit(6, "cm"))
324 324
 ```
325 325
 
326 326
 ## OncoPrint