... | ... |
@@ -1,32 +1,32 @@ |
1 |
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
|
2 |
-setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
1 |
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) |
|
3 | 2 |
setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) |
4 |
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
5 |
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) |
|
3 |
+setGeneric('draw', function(object, ...) standardGeneric('draw')) |
|
6 | 4 |
setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) |
7 |
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) |
|
5 |
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
8 | 6 |
setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) |
9 |
-setGeneric('draw', function(object, ...) standardGeneric('draw')) |
|
10 |
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) |
|
11 | 7 |
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')) |
|
8 |
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) |
|
9 |
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
|
10 |
+setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
|
15 | 11 |
setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) |
12 |
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) |
|
13 |
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) |
|
14 |
+setGeneric('column_order', function(object, ...) standardGeneric('column_order')) |
|
15 |
+setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
16 |
+setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
|
17 |
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size')) |
|
16 | 18 |
setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) |
19 |
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) |
|
20 |
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) |
|
17 | 21 |
setGeneric('component_height', function(object, ...) standardGeneric('component_height')) |
22 |
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation')) |
|
23 |
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) |
|
18 | 24 |
setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) |
19 |
-setGeneric('column_order', function(object, ...) standardGeneric('column_order')) |
|
20 | 25 |
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')) |
|
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 | 26 |
setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) |
27 |
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) |
|
28 |
+setGeneric('prepare', function(object, ...) standardGeneric('prepare')) |
|
29 |
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) |
|
30 |
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) |
|
27 | 31 |
setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) |
28 |
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) |
|
29 |
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) |
|
30 |
-setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
|
31 |
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size')) |
|
32 |
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) |
|
32 |
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) |
... | ... |
@@ -7,9 +7,11 @@ Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/ |
7 | 7 |
Github page: https://github.com/jokergoo/ComplexHeatmap |
8 | 8 |
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference |
9 | 9 |
|
10 |
-If you use it in published research, please cite: |
|
11 |
-Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional |
|
12 |
- genomic data. Bioinformatics 2016. |
|
10 |
+If you use it in published research, please cite either one: |
|
11 |
+- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional |
|
12 |
+ genomic data. Bioinformatics 2016. |
|
13 |
+- Gu, Z. Complex Heatmap Visualization. iMeta 2022. |
|
14 |
+ |
|
13 | 15 |
|
14 | 16 |
The new InteractiveComplexHeatmap package can directly export static |
15 | 17 |
complex heatmaps into an interactive Shiny app with zero effort. Have a try! |
... | ... |
@@ -17,7 +17,9 @@ The [**InteractiveComplexHeatmap**](https://github.com/jokergoo/InteractiveCompl |
17 | 17 |
|
18 | 18 |
## Citation |
19 | 19 |
|
20 |
-Zuguang Gu, et al., [Complex heatmaps reveal patterns and correlations in multidimensional genomic data](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016 |
|
20 |
+Zuguang Gu, et al., [Complex heatmaps reveal patterns and correlations in multidimensional genomic data](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016. |
|
21 |
+ |
|
22 |
+Zuguang Gu. [Complex Heatmap Visualization](https://doi.org/10.1002/imt2.43), iMeta, 2022. |
|
21 | 23 |
|
22 | 24 |
|
23 | 25 |
## Install |
... | ... |
@@ -11,6 +11,17 @@ citEntry( |
11 | 11 |
textVersion = "Gu, Z. (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btw313." |
12 | 12 |
) |
13 | 13 |
|
14 |
+ |
|
15 |
+citEntry( |
|
16 |
+ entry="article", |
|
17 |
+ title = "Complex Heatmap Visualization", |
|
18 |
+ author = personList(as.person("Zuguang Gu")), |
|
19 |
+ journal = "iMeta", |
|
20 |
+ year = 2022, |
|
21 |
+ textVersion = "Gu, Z. (2022) Complex Heatmap Visualization. iMeta. https://doi.org/10.1002/imt2.43." |
|
22 |
+) |
|
23 |
+ |
|
24 |
+ |
|
14 | 25 |
citFooter("This free open-source software implements academic |
15 | 26 |
research by the authors and co-workers. If you use it, |
16 | 27 |
please support the project by citing the appropriate |
... | ... |
@@ -181,8 +181,8 @@ Heatmap(matrix, col, name, |
181 | 181 |
\item{raster_quality}{A value larger than 1.} |
182 | 182 |
\item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .} |
183 | 183 |
\item{raster_resize_mat}{Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image? The value can be logical. If it is \code{TRUE}, \code{\link[base]{mean}} is used to summarize the sub matrix which corresponds to a single pixel. The value can also be a summary function, e.g. \code{\link[base:Extremes]{max}}.} |
184 |
- \item{raster_by_magick}{Whether to use \code{\link[magick]{image_resize}} to scale the image.} |
|
185 |
- \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick]{image_resize}}. A character scalar and all possible values are in \code{\link[magick]{filter_types}}. The default is \code{"Lanczos"}.} |
|
184 |
+ \item{raster_by_magick}{Whether to use \code{\link[magick:transform]{image_resize}} to scale the image.} |
|
185 |
+ \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick:transform]{image_resize}}. A character scalar and all possible values are in \code{\link[magick:options]{filter_types}}. The default is \code{"Lanczos"}.} |
|
186 | 186 |
\item{post_fun}{A function which will be executed after the heatmap list is drawn.} |
187 | 187 |
|
188 | 188 |
} |
... | ... |
@@ -11,8 +11,8 @@ Method dispatch page for \code{add_heatmap}. |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 | 13 |
\item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
-\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 | 14 |
\item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
15 |
+\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
16 | 16 |
} |
17 | 17 |
} |
18 | 18 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{column_dend}. |
10 | 10 |
\code{column_dend} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{column_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{column_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{column_dend,Heatmap-method}}, \code{\link{Heatmap-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,Legends-method}}, \code{\link{Legends-class}} class method |
|
14 | 13 |
\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
14 |
+\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
|
15 |
+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 | 16 |
\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
16 | 17 |
\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 |
|
18 |
+\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method |
|
19 | 19 |
} |
20 | 20 |
} |
21 | 21 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{draw_title}. |
10 | 10 |
\code{draw_title} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{draw_title,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 | 13 |
\item \code{\link{draw_title,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
14 |
+\item \code{\link{draw_title,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{row_dend}. |
10 | 10 |
\code{row_dend} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{row_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 | 13 |
\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
14 |
+\item \code{\link{row_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -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,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 |
-\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
|
13 |
+\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method |
|
15 | 14 |
\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
15 |
+\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
|
16 | 16 |
\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
17 | 17 |
\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
18 |
-\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method |
|
18 |
+\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
19 | 19 |
} |
20 | 20 |
} |
21 | 21 |
\examples{ |