... | ... |
@@ -1,32 +1,32 @@ |
1 |
-setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
|
2 |
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) |
|
3 |
-setGeneric('component_height', function(object, ...) standardGeneric('component_height')) |
|
4 |
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) |
|
5 |
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend')) |
|
6 |
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) |
|
7 |
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) |
|
8 | 1 |
setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
2 |
+setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
3 |
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) |
|
4 |
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
9 | 5 |
setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) |
6 |
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) |
|
7 |
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) |
|
8 |
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) |
|
10 | 9 |
setGeneric('draw', function(object, ...) standardGeneric('draw')) |
11 | 10 |
setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) |
11 |
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend')) |
|
12 |
+setGeneric('prepare', function(object, ...) standardGeneric('prepare')) |
|
13 |
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) |
|
14 |
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) |
|
15 |
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) |
|
16 |
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) |
|
17 |
+setGeneric('component_height', function(object, ...) standardGeneric('component_height')) |
|
18 |
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) |
|
19 |
+setGeneric('column_order', function(object, ...) standardGeneric('column_order')) |
|
20 |
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width')) |
|
21 |
+setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
|
22 |
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) |
|
12 | 23 |
setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) |
24 |
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation')) |
|
25 |
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) |
|
26 |
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) |
|
27 |
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) |
|
13 | 28 |
setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) |
14 |
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
15 | 29 |
setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) |
16 |
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) |
|
30 |
+setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
|
17 | 31 |
setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size')) |
18 |
-setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
|
19 |
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) |
|
20 |
-setGeneric('column_order', function(object, ...) standardGeneric('column_order')) |
|
21 |
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) |
|
22 |
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) |
|
23 |
-setGeneric('prepare', function(object, ...) standardGeneric('prepare')) |
|
24 |
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) |
|
25 | 32 |
setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) |
26 |
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) |
|
27 |
-setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
28 |
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation')) |
|
29 |
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) |
|
30 |
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width')) |
|
31 |
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) |
|
32 |
-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. |
1961 |
+# -max_density Maximal density values in the plot. Normally you don't need to manually set it, but when you have multiple density annotations |
|
1962 |
+# 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") |
1988 | 1990 |
anno_density = function(x, which = c("column", "row"), |
1989 |
- type = c("lines", "violin", "heatmap"), xlim = NULL, |
|
1991 |
+ type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL, |
|
1990 | 1992 |
heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), |
1991 | 1993 |
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 |
|
2045 | 2047 |
if(type == "lines") { |
2046 | 2048 |
xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1]) |
2047 |
- yscale = c(0, max(unlist(density_y))) |
|
2049 |
+ if(is.null(max_density)) { |
|
2050 |
+ yscale = c(0, max(unlist(density_y))) |
|
2051 |
+ } else { |
|
2052 |
+ yscale = c(0, max_density) |
|
2053 |
+ } |
|
2048 | 2054 |
yscale[2] = yscale[2]*1.05 |
2049 | 2055 |
} else if(type == "violin") { |
2050 | 2056 |
xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1]) |
2051 |
- yscale = max(unlist(density_y)) |
|
2057 |
+ if(is.null(max_density)) { |
|
2058 |
+ yscale = max(unlist(density_y)) |
|
2059 |
+ } else { |
|
2060 |
+ yscale = max_density |
|
2061 |
+ } |
|
2052 | 2062 |
yscale = c(-yscale*1.05, yscale*1.05) |
2053 | 2063 |
} else if(type == "heatmap") { |
2054 | 2064 |
yscale = c(0, 1) |
2055 |
- min_y = min(unlist(density_y)) |
|
2056 |
- max_y = max(unlist(density_y)) |
|
2065 |
+ if(is.null(max_density)) { |
|
2066 |
+ min_y = min(unlist(density_y)) |
|
2067 |
+ max_y = max(unlist(density_y)) |
|
2068 |
+ } else { |
|
2069 |
+ min_y = 0 |
|
2070 |
+ max_y = max_density |
|
2071 |
+ } |
|
2057 | 2072 |
col_fun = colorRamp2(seq(min_y, max_y, |
2058 | 2073 |
length.out = length(heatmap_colors)), heatmap_colors) |
2059 | 2074 |
} |
... | ... |
@@ -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{ |
4 | 5 |
Adjust Heatmap List |
5 | 6 |
} |
... | ... |
@@ -23,8 +24,8 @@ This function is only for internal use. |
23 | 24 |
\author{ |
24 | 25 |
Zuguang Gu <z.gu@dkfz.de> |
25 | 26 |
} |
26 |
-\alias{adjust_heatmap_list} |
|
27 | 27 |
\examples{ |
28 | 28 |
# There is no example |
29 | 29 |
NULL |
30 |
+ |
|
30 | 31 |
} |
... | ... |
@@ -8,7 +8,7 @@ Density Annotation |
8 | 8 |
} |
9 | 9 |
\usage{ |
10 | 10 |
anno_density(x, which = c("column", "row"), |
11 |
- type = c("lines", "violin", "heatmap"), xlim = NULL, |
|
11 |
+ 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?} |
... | ... |
@@ -12,7 +12,7 @@ anno_textbox(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAA |
12 | 12 |
} |
13 | 13 |
\arguments{ |
14 | 14 |
|
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.} |
|
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. 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".} |
17 | 17 |
\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} |
3 |
+\alias{annotation_legend_size} |
|
3 | 4 |
\title{ |
4 | 5 |
Size of the Annotation 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{annotation_legend_size} |
|
31 | 31 |
\examples{ |
32 | 32 |
# There is no example |
33 | 33 |
NULL |
34 |
+ |
|
34 | 35 |
} |
... | ... |
@@ -1,5 +1,6 @@ |
1 | 1 |
\name{attach_annotation-Heatmap-method} |
2 | 2 |
\alias{attach_annotation,Heatmap-method} |
3 |
+\alias{attach_annotation} |
|
3 | 4 |
\title{ |
4 | 5 |
Attach heatmap annotations to the heatmap |
5 | 6 |
} |
... | ... |
@@ -28,4 +29,3 @@ ha2 = HeatmapAnnotation(bar = letters[1:10]) |
28 | 29 |
ht = attach_annotation(ht, ha2) |
29 | 30 |
ht |
30 | 31 |
} |
31 |
-\alias{attach_annotation} |
... | ... |
@@ -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 |
} |
... | ... |
@@ -69,8 +70,8 @@ A \code{\link{Legends-class}} object. |
69 | 70 |
\author{ |
70 | 71 |
Zuguang Gu <z.gu@dkfz.de> |
71 | 72 |
} |
72 |
-\alias{color_mapping_legend} |
|
73 | 73 |
\examples{ |
74 | 74 |
# There is no example |
75 | 75 |
NULL |
76 |
+ |
|
76 | 77 |
} |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}. |
10 | 10 |
\code{component_width} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 | 13 |
\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
14 |
+\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}. |
10 | 10 |
\code{draw} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 |
-\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 |
-\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
|
16 | 13 |
\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method |
17 | 14 |
\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
18 | 15 |
\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
16 |
+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
17 |
+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
18 |
+\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-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 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 |
} |
... | ... |
@@ -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 |
} |
... | ... |
@@ -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 |
} |
... | ... |
@@ -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 |
} |
... | ... |
@@ -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} |
... | ... |
@@ -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{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 |
} |
... | ... |
@@ -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 |
} |
... | ... |
@@ -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{ |