@@ -1,8 +1,8 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

-Version: 1.99.1

-Date: 2018-11-23

+Version: 1.99.2

+Date: 2018-11-26

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

@@ -10,7 +10,7 @@ Imports: circlize (>= 0.4.5), GetoptLong, colorspace,

     RColorBrewer, GlobalOptions (>= 0.1.0)

 Suggests: testthat (>= 0.3), knitr, markdown, dendsort, 

     Cairo, png, jpeg, tiff, fastcluster,

-    dendextend (>= 1.0.1), grImport, grImport2, rsvg, glue

+    dendextend (>= 1.0.1), grImport, grImport2, glue

 VignetteBuilder: knitr

 Description: Complex heatmaps are efficient to visualize associations 

     between different sources of data sets and reveal potential patterns. 

@@ -4,6 +4,7 @@ CHANGES in VERSION 1.99.1

 * fixed a bug when annotation_height with only one annotation

 * order of k-means slices are reordered by slice mean of `row_reorder`/`column_reorder`

   if they are provided as vectors.

+* remove **rsvg** from Suggests.

 =======================

@@ -1,31 +1,31 @@

-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

 setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))

-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))

-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

 setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))

 setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))

+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))

+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))

+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

 setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))

-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))

-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

-setGeneric('draw', function(object, ...) standardGeneric('draw'))

+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))

+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

 setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

 setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))

-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))

-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

+setGeneric('draw', function(object, ...) standardGeneric('draw'))

+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

 setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))

+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))

+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))

@@ -337,7 +337,7 @@ anno_simple = function(x, col, na_col = "grey",

 # == details

 # This function supports image formats in ``png``, ``svg``, ``pdf``, ``eps``, ``jpeg/jpg``, ``tiff``. 

 # ``png``, ``jpeg/jpg`` and ``tiff`` images are imported by `png::readPNG`, `jpeg::readJPEG` and 

-# `tiff::readTIFF`, and drawn by `grid::grid.raster`. ``svg`` images are firstly reformatted by `rsvg::rsvg_svg`

+# `tiff::readTIFF`, and drawn by `grid::grid.raster`. ``svg`` images are firstly reformatted by ``rsvg::rsvg_svg``

 # and then imported by `grImport2::readPicture` and drawn by `grImport2::grid.picture`. ``pdf`` and ``eps``

 # images are imported by `grImport::PostScriptTrace` and `grImport::readPicture`, later drawn by `grImport::grid.picture`.

 #

@@ -416,11 +416,15 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,

 			if(!requireNamespace("grImport2")) {

 				stop_wrap("Need grImport2 package to read svg images.")

 			}

-			if(!requireNamespace("rsvg")) {

+			# if(!requireNamespace("rsvg")) {

+			# 	stop_wrap("Need rsvg package to convert svg images.")

+			# }

+			temp_file = tempfile()

+			# get it work on bioconductor build server

+			oe = try(getFromNamespace("rsvg_svg", ns = "rsvg")(image[i], temp_file))

+			if(inherits(oe, "try-error")) {

 				stop_wrap("Need rsvg package to convert svg images.")

 			}

-			temp_file = tempfile()

-			rsvg::rsvg_svg(image[i], temp_file)

 			image_list[[i]] = grImport2::readPicture(temp_file)

 			file.remove(temp_file)

 			image_class[i] = "grImport2::Picture"

@@ -25,7 +25,7 @@ anno_image(image, which = c("column", "row"), border = TRUE,

 \details{

 This function supports image formats in \code{png}, \code{svg}, \code{pdf}, \code{eps}, \code{jpeg/jpg}, \code{tiff}. 

 \code{png}, \code{jpeg/jpg} and \code{tiff} images are imported by \code{\link[png]{readPNG}}, \code{\link[jpeg]{readJPEG}} and 

-\code{\link[tiff]{readTIFF}}, and drawn by \code{\link[grid]{grid.raster}}. \code{svg} images are firstly reformatted by \code{\link[rsvg]{rsvg_svg}}

+\code{\link[tiff]{readTIFF}}, and drawn by \code{\link[grid]{grid.raster}}. \code{svg} images are firstly reformatted by \code{rsvg::rsvg_svg}

 and then imported by \code{\link[grImport2]{readPicture}} and drawn by \code{\link[grImport2]{grid.picture}}. \code{pdf} and \code{eps}

 images are imported by \code{\link[grImport]{PostScriptTrace}} and \code{\link[grImport]{readPicture}}, later drawn by \code{\link[grImport]{grid.picture}}.

@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}.

 \code{component_height} can be dispatched on following classes:

 \itemize{

-\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}.

 \code{component_width} can be dispatched on following classes:

 \itemize{

-\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}.

 \code{draw} can be dispatched on following classes:

 \itemize{

-\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

-\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method

-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

-\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method

 \item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

+\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method

 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

+\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{make_layout}.

 \code{make_layout} can be dispatched on following classes:

 \itemize{

-\item \code{\link{make_layout,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{make_layout,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{make_layout,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{row_order}.

 \code{row_order} can be dispatched on following classes:

 \itemize{

-\item \code{\link{row_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{row_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{row_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,12 +10,12 @@ Method dispatch page for \code{show}.

 \code{show} can be dispatched on following classes:

 \itemize{

-\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method

-\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method

-\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

 \item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

+\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

+\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

+\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{