Zuguang Gu authored on 30/12/2018 08:12:22 | ... | ... |
@@ -955,7 +955,7 @@ order.comb_mat = function(m, decreasing = TRUE, on = "comb_set") {
|
| 955 | 955 |
# |
| 956 | 956 |
upset_top_annotation = function(m, |
| 957 | 957 |
gp = gpar(fill = "black"), |
| 958 |
- height = unit(ifelse(set_on_rows, 2, 3), "cm"), |
|
| 958 |
+ height = unit(ifelse(set_on_rows, 3, 2), "cm"), |
|
| 959 | 959 |
show_annotation_name = TRUE, |
| 960 | 960 |
annotation_name_gp = gpar(), |
| 961 | 961 |
annotation_name_offset = NULL, |
| ... | ... |
@@ -1013,7 +1013,7 @@ upset_top_annotation = function(m, |
| 1013 | 1013 |
# |
| 1014 | 1014 |
upset_right_annotation = function(m, |
| 1015 | 1015 |
gp = gpar(fill = "black"), |
| 1016 |
- width = unit(ifelse(set_on_rows, 3, 2), "cm"), |
|
| 1016 |
+ width = unit(ifelse(set_on_rows, 2, 3), "cm"), |
|
| 1017 | 1017 |
show_annotation_name = TRUE, |
| 1018 | 1018 |
annotation_name_gp = gpar(), |
| 1019 | 1019 |
annotation_name_offset = NULL, |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{adjust_heatmap_list-HeatmapList-method}
|
| 2 | 2 |
\alias{adjust_heatmap_list,HeatmapList-method}
|
| 3 |
-\alias{adjust_heatmap_list}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Adjust Heatmap List |
| 6 | 5 |
} |
| ... | ... |
@@ -24,8 +23,8 @@ This function is only for internal use. |
| 24 | 23 |
\author{
|
| 25 | 24 |
Zuguang Gu <z.gu@dkfz.de> |
| 26 | 25 |
} |
| 26 |
+\alias{adjust_heatmap_list}
|
|
| 27 | 27 |
\examples{
|
| 28 | 28 |
# There is no example |
| 29 | 29 |
NULL |
| 30 |
- |
|
| 31 | 30 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{annotation_legend_size-HeatmapList-method}
|
| 2 | 2 |
\alias{annotation_legend_size,HeatmapList-method}
|
| 3 |
-\alias{annotation_legend_size}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Size of the Annotation Legends |
| 6 | 5 |
} |
| ... | ... |
@@ -28,8 +27,8 @@ A \code{\link[grid]{unit}} object.
|
| 28 | 27 |
\author{
|
| 29 | 28 |
Zuguang Gu <z.gu@dkfz.de> |
| 30 | 29 |
} |
| 30 |
+\alias{annotation_legend_size}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
- |
|
| 35 | 34 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{color_mapping_legend-ColorMapping-method}
|
| 2 | 2 |
\alias{color_mapping_legend,ColorMapping-method}
|
| 3 |
-\alias{color_mapping_legend}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Draw Legend Based on Color Mapping |
| 6 | 5 |
} |
| ... | ... |
@@ -66,8 +65,8 @@ A \code{\link{Legends-class}} object.
|
| 66 | 65 |
\author{
|
| 67 | 66 |
Zuguang Gu <z.gu@dkfz.de> |
| 68 | 67 |
} |
| 68 |
+\alias{color_mapping_legend}
|
|
| 69 | 69 |
\examples{
|
| 70 | 70 |
# There is no example |
| 71 | 71 |
NULL |
| 72 |
- |
|
| 73 | 72 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{draw_annotation-Heatmap-method}
|
| 2 | 2 |
\alias{draw_annotation,Heatmap-method}
|
| 3 |
-\alias{draw_annotation}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Draw Heatmap Annotations on the Heatmap |
| 6 | 5 |
} |
| ... | ... |
@@ -31,8 +30,8 @@ This function returns no value. |
| 31 | 30 |
\author{
|
| 32 | 31 |
Zuguang Gu <z.gu@dkfz.de> |
| 33 | 32 |
} |
| 33 |
+\alias{draw_annotation}
|
|
| 34 | 34 |
\examples{
|
| 35 | 35 |
# There is no example |
| 36 | 36 |
NULL |
| 37 |
- |
|
| 38 | 37 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{draw_annotation_legend-HeatmapList-method}
|
| 2 | 2 |
\alias{draw_annotation_legend,HeatmapList-method}
|
| 3 |
-\alias{draw_annotation_legend}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Draw legends for All Annotations |
| 6 | 5 |
} |
| ... | ... |
@@ -32,8 +31,8 @@ This function returns no value. |
| 32 | 31 |
\author{
|
| 33 | 32 |
Zuguang Gu <z.gu@dkfz.de> |
| 34 | 33 |
} |
| 34 |
+\alias{draw_annotation_legend}
|
|
| 35 | 35 |
\examples{
|
| 36 | 36 |
# There is no example |
| 37 | 37 |
NULL |
| 38 |
- |
|
| 39 | 38 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{draw_dend-Heatmap-method}
|
| 2 | 2 |
\alias{draw_dend,Heatmap-method}
|
| 3 |
-\alias{draw_dend}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Draw Heatmap Dendrograms |
| 6 | 5 |
} |
| ... | ... |
@@ -34,8 +33,8 @@ This function returns no value. |
| 34 | 33 |
\author{
|
| 35 | 34 |
Zuguang Gu <z.gu@dkfz.de> |
| 36 | 35 |
} |
| 36 |
+\alias{draw_dend}
|
|
| 37 | 37 |
\examples{
|
| 38 | 38 |
# There is no example |
| 39 | 39 |
NULL |
| 40 |
- |
|
| 41 | 40 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{draw_dimnames-Heatmap-method}
|
| 2 | 2 |
\alias{draw_dimnames,Heatmap-method}
|
| 3 |
-\alias{draw_dimnames}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Draw row names or column names |
| 6 | 5 |
} |
| ... | ... |
@@ -30,8 +29,8 @@ This function returns no value. |
| 30 | 29 |
\author{
|
| 31 | 30 |
Zuguang Gu <z.gu@dkfz.de> |
| 32 | 31 |
} |
| 32 |
+\alias{draw_dimnames}
|
|
| 33 | 33 |
\examples{
|
| 34 | 34 |
# There is no example |
| 35 | 35 |
NULL |
| 36 |
- |
|
| 37 | 36 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{draw_heatmap_body-Heatmap-method}
|
| 2 | 2 |
\alias{draw_heatmap_body,Heatmap-method}
|
| 3 |
-\alias{draw_heatmap_body}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Draw Heatmap Body |
| 6 | 5 |
} |
| ... | ... |
@@ -29,8 +28,8 @@ This function returns no value. |
| 29 | 28 |
\author{
|
| 30 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 31 | 30 |
} |
| 31 |
+\alias{draw_heatmap_body}
|
|
| 32 | 32 |
\examples{
|
| 33 | 33 |
# There is no example |
| 34 | 34 |
NULL |
| 35 |
- |
|
| 36 | 35 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{draw_heatmap_legend-HeatmapList-method}
|
| 2 | 2 |
\alias{draw_heatmap_legend,HeatmapList-method}
|
| 3 |
-\alias{draw_heatmap_legend}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Draw legends for All Heatmaps |
| 6 | 5 |
} |
| ... | ... |
@@ -33,8 +32,8 @@ This function returns no value. |
| 33 | 32 |
\author{
|
| 34 | 33 |
Zuguang Gu <z.gu@dkfz.de> |
| 35 | 34 |
} |
| 35 |
+\alias{draw_heatmap_legend}
|
|
| 36 | 36 |
\examples{
|
| 37 | 37 |
# There is no example |
| 38 | 38 |
NULL |
| 39 |
- |
|
| 40 | 39 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{draw_heatmap_list-HeatmapList-method}
|
| 2 | 2 |
\alias{draw_heatmap_list,HeatmapList-method}
|
| 3 |
-\alias{draw_heatmap_list}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Draw the List of Heatmaps |
| 6 | 5 |
} |
| ... | ... |
@@ -26,8 +25,8 @@ This function returns no value. |
| 26 | 25 |
\author{
|
| 27 | 26 |
Zuguang Gu <z.gu@dkfz.de> |
| 28 | 27 |
} |
| 28 |
+\alias{draw_heatmap_list}
|
|
| 29 | 29 |
\examples{
|
| 30 | 30 |
# There is no example |
| 31 | 31 |
NULL |
| 32 |
- |
|
| 33 | 32 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{get_color_mapping_list-HeatmapAnnotation-method}
|
| 2 | 2 |
\alias{get_color_mapping_list,HeatmapAnnotation-method}
|
| 3 |
-\alias{get_color_mapping_list}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Get a List of ColorMapping objects |
| 6 | 5 |
} |
| ... | ... |
@@ -26,8 +25,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.
|
| 26 | 25 |
\author{
|
| 27 | 26 |
Zuguang Gu <z.gu@dkfz.de> |
| 28 | 27 |
} |
| 28 |
+\alias{get_color_mapping_list}
|
|
| 29 | 29 |
\examples{
|
| 30 | 30 |
# There is no example |
| 31 | 31 |
NULL |
| 32 |
- |
|
| 33 | 32 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{get_legend_param_list-HeatmapAnnotation-method}
|
| 2 | 2 |
\alias{get_legend_param_list,HeatmapAnnotation-method}
|
| 3 |
-\alias{get_legend_param_list}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Get a List of Annotation Legend Parameters |
| 6 | 5 |
} |
| ... | ... |
@@ -26,8 +25,8 @@ A list. |
| 26 | 25 |
\author{
|
| 27 | 26 |
Zuguang Gu <z.gu@dkfz.de> |
| 28 | 27 |
} |
| 28 |
+\alias{get_legend_param_list}
|
|
| 29 | 29 |
\examples{
|
| 30 | 30 |
# There is no example |
| 31 | 31 |
NULL |
| 32 |
- |
|
| 33 | 32 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{heatmap_legend_size-HeatmapList-method}
|
| 2 | 2 |
\alias{heatmap_legend_size,HeatmapList-method}
|
| 3 |
-\alias{heatmap_legend_size}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Size of the Heatmap Legends |
| 6 | 5 |
} |
| ... | ... |
@@ -28,8 +27,8 @@ A \code{\link[grid]{unit}} object.
|
| 28 | 27 |
\author{
|
| 29 | 28 |
Zuguang Gu <z.gu@dkfz.de> |
| 30 | 29 |
} |
| 30 |
+\alias{heatmap_legend_size}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
- |
|
| 35 | 34 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{make_column_cluster-Heatmap-method}
|
| 2 | 2 |
\alias{make_column_cluster,Heatmap-method}
|
| 3 |
-\alias{make_column_cluster}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Make Cluster on Columns |
| 6 | 5 |
} |
| ... | ... |
@@ -29,8 +28,8 @@ A \code{\link{Heatmap-class}} object.
|
| 29 | 28 |
\author{
|
| 30 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 31 | 30 |
} |
| 31 |
+\alias{make_column_cluster}
|
|
| 32 | 32 |
\examples{
|
| 33 | 33 |
# There is no example |
| 34 | 34 |
NULL |
| 35 |
- |
|
| 36 | 35 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{make_row_cluster-Heatmap-method}
|
| 2 | 2 |
\alias{make_row_cluster,Heatmap-method}
|
| 3 |
-\alias{make_row_cluster}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Make Cluster on Rows |
| 6 | 5 |
} |
| ... | ... |
@@ -28,8 +27,8 @@ A \code{\link{Heatmap-class}} object.
|
| 28 | 27 |
\author{
|
| 29 | 28 |
Zuguang Gu <z.gu@dkfz.de> |
| 30 | 29 |
} |
| 30 |
+\alias{make_row_cluster}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
- |
|
| 35 | 34 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{map_to_colors-ColorMapping-method}
|
| 2 | 2 |
\alias{map_to_colors,ColorMapping-method}
|
| 3 |
-\alias{map_to_colors}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Map Values to Colors |
| 6 | 5 |
} |
| ... | ... |
@@ -35,3 +34,4 @@ col_fun = colorRamp2(c(0, 1), c("white", "red"))
|
| 35 | 34 |
cm = ColorMapping(col_fun = col_fun) |
| 36 | 35 |
map_to_colors(cm, runif(10)) |
| 37 | 36 |
} |
| 37 |
+\alias{map_to_colors}
|
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{prepare-Heatmap-method}
|
| 2 | 2 |
\alias{prepare,Heatmap-method}
|
| 3 |
-\alias{prepare}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Prepare the Heatmap |
| 6 | 5 |
} |
| ... | ... |
@@ -34,8 +33,8 @@ The \code{\link{Heatmap-class}} object.
|
| 34 | 33 |
\author{
|
| 35 | 34 |
Zuguang Gu <z.gu@dkfz.de> |
| 36 | 35 |
} |
| 36 |
+\alias{prepare}
|
|
| 37 | 37 |
\examples{
|
| 38 | 38 |
# There is no example |
| 39 | 39 |
NULL |
| 40 |
- |
|
| 41 | 40 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{re_size-HeatmapAnnotation-method}
|
| 2 | 2 |
\alias{re_size,HeatmapAnnotation-method}
|
| 3 |
-\alias{re_size}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Resize the Width or Height of Heatmap Annotations |
| 6 | 5 |
} |
| ... | ... |
@@ -42,8 +41,8 @@ The basic rules are (take \code{height} and \code{annotation_height} for example
|
| 42 | 41 |
and \code{anno_simple_size} is disabled.
|
| 43 | 42 |
6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.
|
| 44 | 43 |
} |
| 44 |
+\alias{re_size}
|
|
| 45 | 45 |
\examples{
|
| 46 | 46 |
# There is no example |
| 47 | 47 |
NULL |
| 48 |
- |
|
| 49 | 48 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{set_component_height-Heatmap-method}
|
| 2 | 2 |
\alias{set_component_height,Heatmap-method}
|
| 3 |
-\alias{set_component_height}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Set Height of Heatmap Component |
| 6 | 5 |
} |
| ... | ... |
@@ -30,8 +29,8 @@ The \code{\link{Heatmap-class}} object.
|
| 30 | 29 |
\author{
|
| 31 | 30 |
Zuguang Gu <z.gu@dkfz.de> |
| 32 | 31 |
} |
| 32 |
+\alias{set_component_height}
|
|
| 33 | 33 |
\examples{
|
| 34 | 34 |
# There is no example |
| 35 | 35 |
NULL |
| 36 |
- |
|
| 37 | 36 |
} |
| ... | ... |
@@ -1,6 +1,5 @@ |
| 1 | 1 |
\name{set_component_width-Heatmap-method}
|
| 2 | 2 |
\alias{set_component_width,Heatmap-method}
|
| 3 |
-\alias{set_component_width}
|
|
| 4 | 3 |
\title{
|
| 5 | 4 |
Set Width of Heatmap Component |
| 6 | 5 |
} |
| ... | ... |
@@ -29,8 +28,8 @@ The \code{\link{Heatmap-class}} object.
|
| 29 | 28 |
\author{
|
| 30 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 31 | 30 |
} |
| 31 |
+\alias{set_component_width}
|
|
| 32 | 32 |
\examples{
|
| 33 | 33 |
# There is no example |
| 34 | 34 |
NULL |
| 35 |
- |
|
| 36 | 35 |
} |
| ... | ... |
@@ -9,7 +9,7 @@ Default UpSet Right Annotation |
| 9 | 9 |
\usage{
|
| 10 | 10 |
upset_right_annotation(m, |
| 11 | 11 |
gp = gpar(fill = "black"), |
| 12 |
- width = unit(ifelse(set_on_rows, 3, 2), "cm"), |
|
| 12 |
+ width = unit(ifelse(set_on_rows, 2, 3), "cm"), |
|
| 13 | 13 |
show_annotation_name = TRUE, |
| 14 | 14 |
annotation_name_gp = gpar(), |
| 15 | 15 |
annotation_name_offset = NULL, |
| ... | ... |
@@ -37,5 +37,4 @@ how to set the right annotation or left annotation in \code{\link{UpSet}}, pleas
|
| 37 | 37 |
\examples{
|
| 38 | 38 |
# There is no example |
| 39 | 39 |
NULL |
| 40 |
- |
|
| 41 | 40 |
} |
| ... | ... |
@@ -9,7 +9,7 @@ Default UpSet Top Annotation |
| 9 | 9 |
\usage{
|
| 10 | 10 |
upset_top_annotation(m, |
| 11 | 11 |
gp = gpar(fill = "black"), |
| 12 |
- height = unit(ifelse(set_on_rows, 2, 3), "cm"), |
|
| 12 |
+ height = unit(ifelse(set_on_rows, 3, 2), "cm"), |
|
| 13 | 13 |
show_annotation_name = TRUE, |
| 14 | 14 |
annotation_name_gp = gpar(), |
| 15 | 15 |
annotation_name_offset = NULL, |
| ... | ... |
@@ -37,5 +37,4 @@ how to set the top annotation or bottom annotation in \code{\link{UpSet}}, pleas
|
| 37 | 37 |
\examples{
|
| 38 | 38 |
# There is no example |
| 39 | 39 |
NULL |
| 40 |
- |
|
| 41 | 40 |
} |