Browse code

add max_density argument

Zuguang Gu authored on 15/06/2022 10:42:56
Showing147 changed files

... ...
@@ -1,32 +1,32 @@
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-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
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-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
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-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
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-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
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-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
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 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
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+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
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+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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 setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
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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('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
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 setGeneric('draw', function(object, ...) standardGeneric('draw'))
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 setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
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+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
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+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
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+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
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+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
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+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
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+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
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+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
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+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
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+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
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 setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
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+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
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+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
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+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
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+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
13 28
 setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
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-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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 setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
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-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
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+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
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 setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
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-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
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-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
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-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
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-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
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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('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
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-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
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-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
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-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
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-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
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-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
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-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
... ...
@@ -1958,6 +1958,8 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
1958 1958
 # -type Type of graphics to represent density distribution. "lines" for normal density plot; "violine" for violin plot
1959 1959
 #       and "heatmap" for heatmap visualization of density distribution.
1960 1960
 # -xlim Range on x-axis.
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+# -max_density Maximal density values in the plot. Normally you don't need to manually set it, but when you have multiple density annotations
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+#   and you want to compare between them, you should manually set this argument to make density distributions are in a same scale.
1961 1963
 # -heatmap_colors A vector of colors for interpolating density values.
1962 1964
 # -joyplot_scale Relative height of density distribution. A value higher than 1 increases the height of the density
1963 1965
 #               distribution and the plot will represented as so-called "joyplot".
... ...
@@ -1986,7 +1988,7 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
1986 1988
 #     heatmap_colors = c("white", "orange"))
1987 1989
 # draw(anno, test = "heatmap, colors")
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 anno_density = function(x, which = c("column", "row"),
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-	type = c("lines", "violin", "heatmap"), xlim = NULL,
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+	type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL,
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 	heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), 
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 	joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"),
1992 1994
 	axis = TRUE, axis_param = default_axis_param(which),
... ...
@@ -2044,16 +2046,29 @@ anno_density = function(x, which = c("column", "row"),
2044 2046
 	
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 	if(type == "lines") {
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 		xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1])
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-		yscale = c(0, max(unlist(density_y)))
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+		if(is.null(max_density)) {
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+			yscale = c(0, max(unlist(density_y)))
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+		} else {
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+			yscale = c(0, max_density)
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+		}
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 		yscale[2] = yscale[2]*1.05
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 	} else if(type == "violin") {
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 		xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1])
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-		yscale = max(unlist(density_y))
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+		if(is.null(max_density)) {
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+			yscale = max(unlist(density_y))
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+		} else {
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+			yscale = max_density
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+		}
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 		yscale = c(-yscale*1.05, yscale*1.05)
2053 2063
 	} else if(type == "heatmap") {
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 		yscale = c(0, 1)
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-		min_y = min(unlist(density_y))
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-		max_y = max(unlist(density_y))
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+		if(is.null(max_density)) {
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+			min_y = min(unlist(density_y))
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+			max_y = max(unlist(density_y))
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+		} else {
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+			min_y = 0
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+			max_y = max_density
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+		}
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 		col_fun = colorRamp2(seq(min_y, max_y, 
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 			length.out = length(heatmap_colors)), heatmap_colors)
2059 2074
 	}
... ...
@@ -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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 }
... ...
@@ -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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 }
... ...
@@ -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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@@ -22,4 +22,5 @@ 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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 }
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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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@@ -212,4 +212,5 @@ 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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@@ -84,4 +84,5 @@ 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 @@
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 \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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 }
... ...
@@ -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>
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 }
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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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 }
... ...
@@ -8,7 +8,7 @@ Density Annotation
8 8
 }
9 9
 \usage{
10 10
 anno_density(x, which = c("column", "row"),
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-    type = c("lines", "violin", "heatmap"), xlim = NULL,
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+    type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL,
12 12
     heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)),
13 13
     joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"),
14 14
     axis = TRUE, axis_param = default_axis_param(which),
... ...
@@ -20,6 +20,7 @@ anno_density(x, which = c("column", "row"),
20 20
   \item{which}{Whether it is a column annotation or a row annotation?}
21 21
   \item{type}{Type of graphics to represent density distribution. "lines" for normal density plot; "violine" for violin plot and "heatmap" for heatmap visualization of density distribution.}
22 22
   \item{xlim}{Range on x-axis.}
23
+  \item{max_density}{Maximal density values in the plot. Normally you don't need to manually set it, but when you have multiple density annotations and you want to compare between them, you should manually set this argument to make density distributions are in a same scale.}
23 24
   \item{heatmap_colors}{A vector of colors for interpolating density values.}
24 25
   \item{joyplot_scale}{Relative height of density distribution. A value higher than 1 increases the height of the density distribution and the plot will represented as so-called "joyplot".}
25 26
   \item{border}{Wether draw borders of the annotation region?}
... ...
@@ -20,4 +20,5 @@ This function is the same as \code{\link{anno_zoom}}. It links subsets of rows 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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 }
... ...
@@ -36,4 +36,5 @@ 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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 }
... ...
@@ -12,7 +12,7 @@ anno_textbox(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAA
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 }
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 \arguments{
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15
-  \item{align_to}{It controls how the text boxes are aligned to the heatmap rows. The value can be a categorical vector which have the same length as heatmap rows, or a list of row indices.}
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+  \item{align_to}{It controls how the text boxes are aligned to the heatmap rows. The value can be a categorical vector which have the same length as heatmap rows, or a list of row indices. It does not necessarily include all row indices.}
16 16
   \item{text}{The corresponding texts. The value should be a list of texts. To control graphics parameters of texts in the boxes, The value of \code{text} can also be set as a list of data frames where the first column contains the text, from the second column contains graphics parameters for each text. The column names should be "col", "fontsize", "fontfamily" and "fontface".}
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   \item{background_gp}{Graphics for the background.}
18 18
   \item{which}{Only "row" is allowed.}
... ...
@@ -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}
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 \title{
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 Size of the Annotation 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{annotation_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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 }
... ...
@@ -1,5 +1,6 @@
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 \name{attach_annotation-Heatmap-method}
2 2
 \alias{attach_annotation,Heatmap-method}
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+\alias{attach_annotation}
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 \title{
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 Attach heatmap annotations to the heatmap
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 }
... ...
@@ -28,4 +29,3 @@ ha2 = HeatmapAnnotation(bar = letters[1:10])
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 ht = attach_annotation(ht, ha2)
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 ht
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 }
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-\alias{attach_annotation}
... ...
@@ -23,4 +23,5 @@ A \code{\link[GenomicRanges:GRanges-class]{GRanges}} object of the genomic bins.
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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{color_mapping_legend-ColorMapping-method}
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 \alias{color_mapping_legend,ColorMapping-method}
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+\alias{color_mapping_legend}
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 \title{
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 Draw Legend Based on Color Mapping
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 }
... ...
@@ -69,8 +70,8 @@ A \code{\link{Legends-class}} 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{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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 }
... ...
@@ -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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 }
... ...
@@ -20,4 +20,5 @@ If there is no complement set, it returns zero.
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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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@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}.
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 \code{component_width} can be dispatched on following classes:
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 \itemize{
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-\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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 \item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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+\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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 }
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 }
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 \examples{
... ...
@@ -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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 }
... ...
@@ -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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+
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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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@@ -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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 }
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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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@@ -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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 }
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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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 }
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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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 }
... ...
@@ -20,4 +20,5 @@ It recognizes following separators: \code{;:,|}.
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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 @@ 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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 }
... ...
@@ -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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 }
... ...
@@ -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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@@ -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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 }
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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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 }
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 }
... ...
@@ -209,4 +209,5 @@ Zuguang Gu <z.gu@dkfz.de>
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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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 }
... ...
@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}.
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 \code{draw} can be dispatched on following classes:
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 \itemize{
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-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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-\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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-\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
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 \item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method
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 \item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
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 \item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
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+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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+\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
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 }
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 }
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 \examples{
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation-Heatmap-method}
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 \alias{draw_annotation,Heatmap-method}
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+\alias{draw_annotation}
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 \title{
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 Draw Heatmap Annotations on the Heatmap
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 }
... ...
@@ -30,8 +31,8 @@ This function returns no value.
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 \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 Annotations
5 6
 }
... ...
@@ -31,8 +32,8 @@ This function returns no value.
31 32
 \author{
32 33
 Zuguang Gu <z.gu@dkfz.de>
33 34
 }
34
-\alias{draw_annotation_legend}
35 35
 \examples{
36 36
 # There is no example
37 37
 NULL
38
+
38 39
 }
... ...
@@ -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 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
 }
... ...
@@ -32,8 +33,8 @@ This function returns no value.
32 33
 \author{
33 34
 Zuguang Gu <z.gu@dkfz.de>
34 35
 }
35
-\alias{draw_heatmap_legend}
36 36
 \examples{
37 37
 # There is no example
38 38
 NULL
39
+
39 40
 }
... ...
@@ -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
 }
... ...
@@ -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
 }
... ...
@@ -24,4 +24,5 @@ All details can be found in the help page of \code{\link{textbox_grob}}.
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -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 Legends
5 6
 }
... ...
@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{heatmap_legend_size}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -18,4 +18,5 @@ Height 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 @@ Height 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 height of the grob can be get by \code{convertWidth(grobHeight(axis
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -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
 }
... ...
@@ -20,4 +20,5 @@ A \code{\link[grid]{unit}} object.
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -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
 }
... ...
@@ -20,4 +20,5 @@ A list of two elements: width and height.
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -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
 }
... ...
@@ -20,4 +20,5 @@ A vector of viewport names.
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -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
 }
... ...
@@ -155,4 +155,5 @@ Zuguang Gu <z.gu@dkfz.de>
155 155
 \examples{
156 156
 # There is no example
157 157
 NULL
158
+
158 159
 }
... ...
@@ -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
 }
... ...
@@ -24,4 +24,5 @@ The sets (by \code{\link{set_name}}) from all combination matrice should be the
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -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
 }
... ...
@@ -95,4 +95,5 @@ Zuguang Gu <z.gu@dkfz.de>
95 95
 \examples{
96 96
 # There is no example
97 97
 NULL
98
+
98 99
 }
... ...
@@ -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
 }
... ...
@@ -148,4 +148,5 @@ A \code{\link{Heatmap-class}} object.
148 148
 \examples{
149 149
 # There is no example
150 150
 NULL
151
+
151 152
 }
... ...
@@ -18,4 +18,5 @@ Draw heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ Draw heatmap annotations
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ Draw heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -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{simple_anno_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_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
 }
... ...
@@ -10,12 +10,12 @@ 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,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
13
+\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14 14
 \item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
15
+\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
15 16
 \item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
16
-\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
17 17
 \item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
18
-\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
18
+\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
19 19
 }
20 20
 }
21 21
 \examples{
... ...
@@ -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
 }
... ...
@@ -18,4 +18,5 @@ str method
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -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
 }
... ...
@@ -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
 }
... ...
@@ -35,4 +35,5 @@ upset_left_annotation(m,
35 35
 \examples{
36 36
 # There is no example
37 37
 NULL
38
+
38 39
 }
... ...
@@ -41,4 +41,5 @@ and if under the union mode, it is \code{union_size}.
41 41
 \examples{
42 42
 # There is no example
43 43
 NULL
44
+
44 45
 }
... ...
@@ -41,4 +41,5 @@ and if under the union mode, it is \code{union_size}.
41 41
 \examples{
42 42
 # There is no example
43 43
 NULL
44
+
44 45
 }
... ...
@@ -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
 }
... ...
@@ -20,4 +20,5 @@ A \code{\link[grid]{unit}} object.
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }