... | ... |
@@ -1,8 +1,8 @@ |
1 | 1 |
Package: ComplexHeatmap |
2 | 2 |
Type: Package |
3 | 3 |
Title: Make Complex Heatmaps |
4 |
-Version: 1.99.1 |
|
5 |
-Date: 2018-11-23 |
|
4 |
+Version: 1.99.2 |
|
5 |
+Date: 2018-11-26 |
|
6 | 6 |
Author: Zuguang Gu |
7 | 7 |
Maintainer: Zuguang Gu <z.gu@dkfz.de> |
8 | 8 |
Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices |
... | ... |
@@ -10,7 +10,7 @@ Imports: circlize (>= 0.4.5), GetoptLong, colorspace, |
10 | 10 |
RColorBrewer, GlobalOptions (>= 0.1.0) |
11 | 11 |
Suggests: testthat (>= 0.3), knitr, markdown, dendsort, |
12 | 12 |
Cairo, png, jpeg, tiff, fastcluster, |
13 |
- dendextend (>= 1.0.1), grImport, grImport2, rsvg, glue |
|
13 |
+ dendextend (>= 1.0.1), grImport, grImport2, glue |
|
14 | 14 |
VignetteBuilder: knitr |
15 | 15 |
Description: Complex heatmaps are efficient to visualize associations |
16 | 16 |
between different sources of data sets and reveal potential patterns. |
... | ... |
@@ -4,6 +4,7 @@ CHANGES in VERSION 1.99.1 |
4 | 4 |
* fixed a bug when annotation_height with only one annotation |
5 | 5 |
* order of k-means slices are reordered by slice mean of `row_reorder`/`column_reorder` |
6 | 6 |
if they are provided as vectors. |
7 |
+* remove **rsvg** from Suggests. |
|
7 | 8 |
|
8 | 9 |
======================= |
9 | 10 |
|
... | ... |
@@ -1,31 +1,31 @@ |
1 |
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
1 |
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) |
|
2 | 2 |
setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) |
3 |
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) |
|
4 |
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) |
|
5 |
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
|
6 |
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) |
|
7 |
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) |
|
8 |
-setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
3 |
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
9 | 4 |
setGeneric('component_height', function(object, ...) standardGeneric('component_height')) |
5 |
+setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
|
10 | 6 |
setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) |
11 |
-setGeneric('column_order', function(object, ...) standardGeneric('column_order')) |
|
7 |
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) |
|
8 |
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) |
|
9 |
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend')) |
|
10 |
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) |
|
11 |
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) |
|
12 |
+setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
13 |
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) |
|
14 |
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) |
|
15 |
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) |
|
12 | 16 |
setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width')) |
13 |
-setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
|
14 |
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) |
|
15 |
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) |
|
16 |
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) |
|
17 |
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) |
|
18 |
-setGeneric('draw', function(object, ...) standardGeneric('draw')) |
|
17 |
+setGeneric('column_order', function(object, ...) standardGeneric('column_order')) |
|
18 |
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) |
|
19 |
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) |
|
19 | 20 |
setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size')) |
20 |
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) |
|
21 | 21 |
setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) |
22 | 22 |
setGeneric('prepare', function(object, ...) standardGeneric('prepare')) |
23 | 23 |
setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) |
24 |
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) |
|
25 |
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) |
|
26 |
-setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
|
27 |
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) |
|
28 |
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) |
|
29 |
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) |
|
30 |
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend')) |
|
24 |
+setGeneric('draw', function(object, ...) standardGeneric('draw')) |
|
25 |
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
|
26 |
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) |
|
27 |
+setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
|
28 |
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) |
|
31 | 29 |
setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) |
30 |
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) |
|
31 |
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) |
... | ... |
@@ -337,7 +337,7 @@ anno_simple = function(x, col, na_col = "grey", |
337 | 337 |
# == details |
338 | 338 |
# This function supports image formats in ``png``, ``svg``, ``pdf``, ``eps``, ``jpeg/jpg``, ``tiff``. |
339 | 339 |
# ``png``, ``jpeg/jpg`` and ``tiff`` images are imported by `png::readPNG`, `jpeg::readJPEG` and |
340 |
-# `tiff::readTIFF`, and drawn by `grid::grid.raster`. ``svg`` images are firstly reformatted by `rsvg::rsvg_svg` |
|
340 |
+# `tiff::readTIFF`, and drawn by `grid::grid.raster`. ``svg`` images are firstly reformatted by ``rsvg::rsvg_svg`` |
|
341 | 341 |
# and then imported by `grImport2::readPicture` and drawn by `grImport2::grid.picture`. ``pdf`` and ``eps`` |
342 | 342 |
# images are imported by `grImport::PostScriptTrace` and `grImport::readPicture`, later drawn by `grImport::grid.picture`. |
343 | 343 |
# |
... | ... |
@@ -416,11 +416,15 @@ anno_image = function(image, which = c("column", "row"), border = TRUE, |
416 | 416 |
if(!requireNamespace("grImport2")) { |
417 | 417 |
stop_wrap("Need grImport2 package to read svg images.") |
418 | 418 |
} |
419 |
- if(!requireNamespace("rsvg")) { |
|
419 |
+ # if(!requireNamespace("rsvg")) { |
|
420 |
+ # stop_wrap("Need rsvg package to convert svg images.") |
|
421 |
+ # } |
|
422 |
+ temp_file = tempfile() |
|
423 |
+ # get it work on bioconductor build server |
|
424 |
+ oe = try(getFromNamespace("rsvg_svg", ns = "rsvg")(image[i], temp_file)) |
|
425 |
+ if(inherits(oe, "try-error")) { |
|
420 | 426 |
stop_wrap("Need rsvg package to convert svg images.") |
421 | 427 |
} |
422 |
- temp_file = tempfile() |
|
423 |
- rsvg::rsvg_svg(image[i], temp_file) |
|
424 | 428 |
image_list[[i]] = grImport2::readPicture(temp_file) |
425 | 429 |
file.remove(temp_file) |
426 | 430 |
image_class[i] = "grImport2::Picture" |
... | ... |
@@ -25,7 +25,7 @@ anno_image(image, which = c("column", "row"), border = TRUE, |
25 | 25 |
\details{ |
26 | 26 |
This function supports image formats in \code{png}, \code{svg}, \code{pdf}, \code{eps}, \code{jpeg/jpg}, \code{tiff}. |
27 | 27 |
\code{png}, \code{jpeg/jpg} and \code{tiff} images are imported by \code{\link[png]{readPNG}}, \code{\link[jpeg]{readJPEG}} and |
28 |
-\code{\link[tiff]{readTIFF}}, and drawn by \code{\link[grid]{grid.raster}}. \code{svg} images are firstly reformatted by \code{\link[rsvg]{rsvg_svg}} |
|
28 |
+\code{\link[tiff]{readTIFF}}, and drawn by \code{\link[grid]{grid.raster}}. \code{svg} images are firstly reformatted by \code{rsvg::rsvg_svg} |
|
29 | 29 |
and then imported by \code{\link[grImport2]{readPicture}} and drawn by \code{\link[grImport2]{grid.picture}}. \code{pdf} and \code{eps} |
30 | 30 |
images are imported by \code{\link[grImport]{PostScriptTrace}} and \code{\link[grImport]{readPicture}}, later drawn by \code{\link[grImport]{grid.picture}}. |
31 | 31 |
|
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}. |
10 | 10 |
\code{component_height} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -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,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{component_width,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,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
|
14 |
-\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 |
-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
16 |
-\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method |
|
17 | 13 |
\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
14 |
+\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method |
|
18 | 15 |
\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
16 |
+\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
|
17 |
+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
18 |
+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
19 | 19 |
} |
20 | 20 |
} |
21 | 21 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{make_layout}. |
10 | 10 |
\code{make_layout} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{make_layout,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{make_layout,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{make_layout,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{row_order}. |
10 | 10 |
\code{row_order} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{row_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{row_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{row_order,Heatmap-method}}, \code{\link{Heatmap-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 |
|
15 |
-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
16 | 13 |
\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method |
17 |
-\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
|
18 | 14 |
\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
15 |
+\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
|
16 |
+\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
|
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 |
|
19 | 19 |
} |
20 | 20 |
} |
21 | 21 |
\examples{ |