add max_density argument

R/00_S4_generic_methods.R

@@ -1,32 +1,32 @@
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
 setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
 setGeneric('draw', function(object, ...) standardGeneric('draw'))
 setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
 setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
 setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
 setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
 setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
 setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

R/AnnotationFunction-function.R

@@ -1958,6 +1958,8 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
 # -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.
 # -xlim Range on x-axis.
+# -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.
 # -heatmap_colors A vector of colors for interpolating density values.
 # -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".
@@ -1986,7 +1988,7 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
 #     heatmap_colors = c("white", "orange"))
 # draw(anno, test = "heatmap, colors")
 anno_density = function(x, which = c("column", "row"),
-	type = c("lines", "violin", "heatmap"), xlim = NULL,
+	type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL,
 	heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), 
 	joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"),
 	axis = TRUE, axis_param = default_axis_param(which),
@@ -2044,16 +2046,29 @@ anno_density = function(x, which = c("column", "row"),
 
 	if(type == "lines") {
 		xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1])
-		yscale = c(0, max(unlist(density_y)))
+		if(is.null(max_density)) {
+			yscale = c(0, max(unlist(density_y)))
+		} else {
+			yscale = c(0, max_density)
+		}
 		yscale[2] = yscale[2]*1.05
 	} else if(type == "violin") {
 		xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1])
-		yscale = max(unlist(density_y))
+		if(is.null(max_density)) {
+			yscale = max(unlist(density_y))
+		} else {
+			yscale = max_density
+		}
 		yscale = c(-yscale*1.05, yscale*1.05)
 	} else if(type == "heatmap") {
 		yscale = c(0, 1)
-		min_y = min(unlist(density_y))
-		max_y = max(unlist(density_y))
+		if(is.null(max_density)) {
+			min_y = min(unlist(density_y))
+			max_y = max(unlist(density_y))
+		} else {
+			min_y = 0
+			max_y = max_density
+		}
 		col_fun = colorRamp2(seq(min_y, max_y, 
 			length.out = length(heatmap_colors)), heatmap_colors)
 	}

man/AdditiveUnit-class.Rd

@@ -15,4 +15,5 @@ method and the \code{\%v\%v} method so that above three classes can be appended
 \examples{
 # There is no example
 NULL
+
 }

man/AdditiveUnit.Rd

@@ -26,4 +26,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/AnnotationFunction-class.Rd

@@ -22,4 +22,5 @@ See \code{\link{AnnotationFunction}} constructor for details.
 \examples{
 # There is no example
 NULL
+
 }

man/ColorMapping-class.Rd

@@ -26,4 +26,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/ComplexHeatmap-package.Rd

@@ -40,4 +40,5 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok
 \examples{
 # There is no example
 NULL
+
 }

man/Extract.gridtext.Rd

@@ -22,4 +22,5 @@ Internally used.
 \examples{
 # There is no example
 NULL
+
 }

man/Heatmap-class.Rd

@@ -30,4 +30,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/Heatmap.Rd

@@ -212,4 +212,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/HeatmapAnnotation-class.Rd

@@ -25,4 +25,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/HeatmapAnnotation.Rd

@@ -84,4 +84,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/HeatmapList-class.Rd

@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/HeatmapList.Rd

@@ -26,4 +26,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/Legends.Rd

@@ -26,4 +26,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/SingleAnnotation-class.Rd

@@ -28,4 +28,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/add.AdditiveUnit.Rd

@@ -40,4 +40,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/add_heatmap-Heatmap-method.Rd

@@ -28,4 +28,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/add_heatmap-HeatmapAnnotation-method.Rd

@@ -28,4 +28,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/add_heatmap-HeatmapList-method.Rd

@@ -28,4 +28,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/adjust_heatmap_list-HeatmapList-method.Rd

@@ -1,5 +1,6 @@
 \name{adjust_heatmap_list-HeatmapList-method}
 \alias{adjust_heatmap_list,HeatmapList-method}
+\alias{adjust_heatmap_list}
 \title{
 Adjust Heatmap List
 }
@@ -23,8 +24,8 @@ This function is only for internal use.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{adjust_heatmap_list}
 \examples{
 # There is no example
 NULL
+
 }

man/anno_density.Rd

@@ -8,7 +8,7 @@ Density Annotation
 }
 \usage{
 anno_density(x, which = c("column", "row"),
-    type = c("lines", "violin", "heatmap"), xlim = NULL,
+    type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL,
     heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)),
     joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"),
     axis = TRUE, axis_param = default_axis_param(which),
@@ -20,6 +20,7 @@ anno_density(x, which = c("column", "row"),
   \item{which}{Whether it is a column annotation or a row annotation?}
   \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.}
   \item{xlim}{Range on x-axis.}
+  \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.}
   \item{heatmap_colors}{A vector of colors for interpolating density values.}
   \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".}
   \item{border}{Wether draw borders of the annotation region?}

man/anno_link.Rd

@@ -20,4 +20,5 @@ This function is the same as \code{\link{anno_zoom}}. It links subsets of rows o
 \examples{
 # There is no example
 NULL
+
 }

man/anno_oncoprint_barplot.Rd

@@ -36,4 +36,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/anno_textbox.Rd

@@ -12,7 +12,7 @@ anno_textbox(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAA
 }
 \arguments{
 
-  \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.}
+  \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.}
   \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".}
   \item{background_gp}{Graphics for the background.}
   \item{which}{Only "row" is allowed.}

man/annotation_legend_size-HeatmapList-method.Rd

@@ -1,5 +1,6 @@
 \name{annotation_legend_size-HeatmapList-method}
 \alias{annotation_legend_size,HeatmapList-method}
+\alias{annotation_legend_size}
 \title{
 Size of the Annotation Legends
 }
@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{annotation_legend_size}
 \examples{
 # There is no example
 NULL
+
 }

man/attach_annotation-Heatmap-method.Rd

@@ -1,5 +1,6 @@
 \name{attach_annotation-Heatmap-method}
 \alias{attach_annotation,Heatmap-method}
+\alias{attach_annotation}
 \title{
 Attach heatmap annotations to the heatmap
 }
@@ -28,4 +29,3 @@ ha2 = HeatmapAnnotation(bar = letters[1:10])
 ht = attach_annotation(ht, ha2)
 ht
 }
-\alias{attach_annotation}

man/bin_genome.Rd

@@ -23,4 +23,5 @@ A \code{\link[GenomicRanges:GRanges-class]{GRanges}} object of the genomic bins.
 \examples{
 # There is no example
 NULL
+
 }

man/color_mapping_legend-ColorMapping-method.Rd

@@ -1,5 +1,6 @@
 \name{color_mapping_legend-ColorMapping-method}
 \alias{color_mapping_legend,ColorMapping-method}
+\alias{color_mapping_legend}
 \title{
 Draw Legend Based on Color Mapping
 }
@@ -69,8 +70,8 @@ A \code{\link{Legends-class}} object.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{color_mapping_legend}
 \examples{
 # There is no example
 NULL
+
 }

man/columnAnnotation.Rd

@@ -29,4 +29,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/complement_size.Rd

@@ -20,4 +20,5 @@ If there is no complement set, it returns zero.
 \examples{
 # There is no example
 NULL
+
 }

man/component_height-Heatmap-method.Rd

@@ -31,4 +31,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/component_height-HeatmapList-method.Rd

@@ -24,4 +24,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/component_width-Heatmap-method.Rd

@@ -30,4 +30,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/component_width-HeatmapList-method.Rd

@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/component_width-dispatch.Rd

@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}.
 \code{component_width} can be dispatched on following classes:
 
 \itemize{
-\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
 \item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
+\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
 }
 }
 \examples{

man/copy_all-AnnotationFunction-method.Rd

@@ -26,4 +26,5 @@ The environment is at \code{object@var_env}.
 \examples{
 # There is no example
 NULL
+
 }

man/copy_all-SingleAnnotation-method.Rd

@@ -21,4 +21,5 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia
 \examples{
 # There is no example
 NULL
+
 }

man/decorate_column_dend.Rd

@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/decorate_column_names.Rd

@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }

man/decorate_column_title.Rd

@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }