Zuguang Gu authored on 20/10/2019 06:57:30 | ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
CHANGES in VERSION 2.1.1 |
| 2 | 2 |
|
| 3 | 3 |
* `Heatmap()`: give error when heatmap has empty string as its name. |
| 4 |
-* `anno_mark()`: text positions are correctly calcualted now with rotations. |
|
| 4 |
+* `anno_mark()`: text positions are correctly calculated now with rotations. |
|
| 5 | 5 |
|
| 6 | 6 |
======================== |
| 7 | 7 |
|
| ... | ... |
@@ -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 |
} |
| ... | ... |
@@ -10,7 +10,7 @@ Link annotation with labels |
| 10 | 10 |
anno_mark(at, labels, which = c("column", "row"),
|
| 11 | 11 |
side = ifelse(which == "column", "top", "right"), |
| 12 | 12 |
lines_gp = gpar(), labels_gp = gpar(), |
| 13 |
- labels_rot = ifelse(which == "column", 90, 0), padding = 0.5, |
|
| 13 |
+ labels_rot = ifelse(which == "column", 90, 0), padding = unit(1, "mm"), |
|
| 14 | 14 |
link_width = unit(5, "mm"), link_height = link_width, |
| 15 | 15 |
link_gp = lines_gp, |
| 16 | 16 |
extend = unit(0, "mm")) |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{annotation_legend_size-HeatmapList-method}
|
| 2 | 2 |
\alias{annotation_legend_size,HeatmapList-method}
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| 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{color_mapping_legend-ColorMapping-method}
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| 2 | 2 |
\alias{color_mapping_legend,ColorMapping-method}
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| 3 |
+\alias{color_mapping_legend}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw Legend Based on Color Mapping |
| 5 | 6 |
} |
| ... | ... |
@@ -65,8 +66,8 @@ A \code{\link{Legends-class}} object.
|
| 65 | 66 |
\author{
|
| 66 | 67 |
Zuguang Gu <z.gu@dkfz.de> |
| 67 | 68 |
} |
| 68 |
-\alias{color_mapping_legend}
|
|
| 69 | 69 |
\examples{
|
| 70 | 70 |
# There is no example |
| 71 | 71 |
NULL |
| 72 |
+ |
|
| 72 | 73 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{draw_annotation-Heatmap-method}
|
| 2 | 2 |
\alias{draw_annotation,Heatmap-method}
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| 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}
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| 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}
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| 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}
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| 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}
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| 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}
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| 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}
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| 2 | 2 |
\alias{make_row_cluster,Heatmap-method}
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| 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}
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| 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}
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| 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}
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| 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}
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| 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}
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| 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 |
} |