@@ -2,7 +2,7 @@ Package: ComplexHeatmap

 Type: Package

 Title: Making Complex Heatmaps

 Version: 1.9.3

-Date: 2016-1-7

+Date: 2016-3-6

 Author: Zuguang Gu

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

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

@@ -18,6 +18,6 @@ Description: Complex heatmaps are efficient to visualize associations

 biocViews: Software, Visualization, Sequencing

 URL: https://github.com/jokergoo/ComplexHeatmap

 License: GPL (>= 2)

-Packaged: 2016-1-7 00:00:00 UTC; Administrator

+Packaged: 2016-3-6 00:00:00 UTC; Administrator

 Repository: Bioconductor

-Date/Publication: 2016-1-7 00:00:00

+Date/Publication: 2016-3-6 00:00:00

@@ -1,21 +1,21 @@

-CHANEGS in VERSION 1.9.3

+CHANGES in VERSION 1.9.3

 * graphic parameters are correctly recycled in row annotations

 * if there is only one row after splitting, there will be no dendrogram

 * add `range` option in `densityHeatmap()`

 * when `gap` is set for the main heatmap, other heatmps also adjust their `gap` values to it

 * fixed a bug that when rownames/colnames are not complete, dendrograms are corrupted

-* `alter_fun` now support adding graphics grid by grid

+* `alter_fun` now supports adding graphics grid by grid

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

-CHANEGS in VERSION 1.9.2

+CHANGES in VERSION 1.9.2

 * imporved example of `anno_link()`

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

-CHANEGS in VERSION 1.9.1

+CHANGES in VERSION 1.9.1

 * width of the heatmap body are calculated correctly if it is set as a fixed unit

 * there is no dendrogram is nrows in a row-slice is 1

@@ -56,6 +56,10 @@

 # - `Heatmap`: constructor method.

 # - `draw,Heatmap-method`: draw a single heatmap.

 # - `add_heatmap,Heatmap-method` append heatmaps and row annotations to a list of heatmaps.

+# - `row_order,HeatmapList-method`: get order of rows

+# - `column_order,HeatmapList-method`: get order of columns

+# - `row_dend,HeatmapList-method`: get row dendrograms

+# - `column_dend,HeatmapList-method`: get column dendrograms

 #

 # == author

 # Zuguang Gu <z.gu@dkfz.de>

@@ -44,7 +44,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # -na_col color for ``NA`` values in simple annotations.

 # -annotation_legend_param a list which contains parameters for annotation legends

 # -show_legend whether show legend for each column in ``df``.

-# -... functions which define complex annotations. Values should be named arguments.

+# -... functions which define complex annotations or vectors of simple annotation. Values should be named arguments.

 # -which are the annotations row annotations or column annotations?

 # -annotation_height height of each annotation if annotations are column annotations.

 # -annotation_width width of each annotation if annotations are row annotations.

@@ -44,7 +44,11 @@

 # The `HeatmapList-class` provides following methods:

 #

 # - `draw,HeatmapList-method`: draw the list of heatmaps and row annotations.

-# - `add_heatmap,HeatmapList-method` add heatmaps to the list of heatmaps.

+# - `add_heatmap,HeatmapList-method`: add heatmaps to the list of heatmaps.

+# - `row_order,HeatmapList-method`: get order of rows

+# - `column_order,HeatmapList-method`: get order of columns

+# - `row_dend,HeatmapList-method`: get row dendrograms

+# - `column_dend,HeatmapList-method`: get column dendrograms

 #

 # == author

 # Zuguang Gu <z.gu@dkfz.de>

@@ -12,7 +12,7 @@

 # goes to the viewport by `grid::seekViewport` and applies code

 # to that viewport.

 #

-# Since you know the number of rows and columns for that row slice, it is

+# If you know the number of rows and columns for that row slice, it is

 # simple to calculate the position of every small grid in the row slice.

 # E.g., the position for the grid in i^th row and j^th column is:

 #

@@ -73,7 +73,7 @@ decorate_heatmap_body = function(heatmap, code, slice = 1) {

 # goes to the viewport by `grid::seekViewport` and applies code

 # to that viewport.

 #

-# Since you know the number of leaves in the dendrogram, it is

+# If you know the number of leaves in the dendrogram, it is

 # simple to calculate the position of every leave in the dendrogram.

 # E.g., for the column dendrogram, the i^th leave is located at:

 #

@@ -179,7 +179,7 @@ decorate_row_dend = function(...) {

 # goes to the viewport by `grid::seekViewport` and applies code

 # to that viewport.

 #

-# Since you know the dimensions of the matrix, it is

+# If you know the dimensions of the matrix, it is

 # simple to calculate the position of every row name or column name in the heatmap.

 # E.g., for the column column, the i^th name is located at:

 #

@@ -4,14 +4,14 @@

 #

 # == param

 # -data  a matrix or a list. If it is a matrix, density will be calculated by columns.

-# -col a list of colors that density values are scaled to.

+# -col a list of colors that density values are mapped to.

 # -color_space the color space in which colors are interpolated. Pass to `circlize::colorRamp2`.

-# -anno annotation for the matrix columns or the list. The value should be a vector or a data frame. 

-#       It can also be a `HeatmapAnnotation-class` object.

+# -anno annotation for the matrix columns or the list. The value should be a vector or a data frame 

+#       and colors for annotations are randomly assigned. If you want to customize the annotation colors,

+#       use a `HeatmapAnnotation-class` object directly.

 # -ylab label on y-axis in the plot

 # -title title of the plot

-# -range ranges on the y-axis. The lower bound is the maximul value between ``range[[1]]`` and minimal value

-#        in the data and the upper bound is the minimal value between ``range[[2]]`` and maximul value in the data.

+# -range ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.

 # -... pass to `draw,HeatmapList-method`

 #

 # == details

@@ -32,7 +32,8 @@

 # densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))

 # densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))

 #

-# ha = HeatmapAnnotation(points = anno_points(runif(10)))

+# ha = HeatmapAnnotation(points = anno_points(runif(10)),

+#     anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))

 # densityHeatmap(matrix, anno = ha)

 #

 # lt = list(rnorm(10), rnorm(10))

@@ -60,8 +61,8 @@ densityHeatmap = function(data,

 	n = length(density_list)

 	nm = names(density_list)

-	max_x = max(unlist(lapply(density_list, function(x) x$x)))

-	min_x = min(unlist(lapply(density_list, function(x) x$x)))

+	max_x = quantile(unlist(lapply(density_list, function(x) x$x)), 0.99)

+	min_x = quantile(unlist(lapply(density_list, function(x) x$x)), 0.01)

 	max_x = min(max_x, range[2])

 	min_x = max(min_x, range[1])

@@ -258,7 +258,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 	dimnames(pheudo) = dimnames(arr)[1:2]

 	if(length(list(...))) {

-		if(names(list(...)) %in% c("rect_gp", "cluster_rows", "cluster_columns", "cell_fun")) {

+		if(any(names(list(...)) %in% c("rect_gp", "cluster_rows", "cluster_columns", "cell_fun"))) {

 			stop("'rect_gp', 'cluster_rows', 'cluster_columns', 'cell_fun' are not allowed to use in `oncoPrint()`.")

 		}

 	}

@@ -9,7 +9,7 @@

 # Users can use mouse to click two positions on the heatmap, the function

 # will return the row index and column index for the selected region in the selected matrix.

 #

-# Of cource this function only works under interactive graphical environment.

+# This function only works under interactive graphical environment.

 #

 # == value

 # A list containing row index and column index corresponding to the selected region.

@@ -90,7 +90,7 @@ to specific target regions.

 There are several vignettes in the package. Each vignette focuses on a specific topic. Following

 lists the general topics discussed in these vignettes:

-  1. [**Making a Single Heatmap**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html)

+  1. [**Making a Single Heatmap**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html)

     This vignette introduces the basic configuration for making a single heatmap. Similar as other

     R functions/packages, the basic usage is quite similar, but there are several unique features

@@ -112,36 +112,36 @@ lists the general topics discussed in these vignettes:

       different levels that split the heatmap.

     - The heatmap body itself can be completely self-defined.

-  2. [**Making a List of Heatmaps**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)

+  2. [**Making a List of Heatmaps**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)

     This vignette introduces how to concatenate a list of heatmaps and how adjustment is applied to keep

     the correspondence of the heatmaps.

-  3. [**Heatmap Annotations**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html)

+  3. [**Heatmap Annotations**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html)

     This vignette introduces the concept of the heatmap annotation and demonstrate how to make simple annotations

     as well as complex annotations. Also, the vignette explains the difference between column annotations

     and row annotations.

-  4. [**Heatmap and Annotation Legends**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s5.legend.html)

+  4. [**Heatmap and Annotation Legends**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s5.legend.html)

     This vignette introduces how to configurate the heatmap legend and annotation legend, also

     how to add self-defined legends.

-  5. [**Heatmap Decoration**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s6.heatmap_decoration.html)

+  5. [**Heatmap Decoration**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s6.heatmap_decoration.html)

     This vignette introduces methods to add more self-defined graphics to the heatmaps after the heatmaps

     are generated.

-  6. [**Interactive with Heatmaps**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s7.interactive.html)

+  6. [**Interactive with Heatmaps**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s7.interactive.html)

     How to select a region in the heatmap to retrieve the sub-matrix.

-  7. [**OncoPrint**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s8.oncoprint.html)

+  7. [**OncoPrint**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s8.oncoprint.html)

     How to make an oncoPrint.

-  8. [**Examples**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s9.examples.html)

+  8. [**Examples**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s9.examples.html)

     More simulated and real-world examples are shown in this vignette.

new file mode 100644

@@ -60,6 +60,10 @@ The \code{\link{Heatmap-class}} provides following methods:

   \item \code{\link{Heatmap}}: constructor method.

   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.

   \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.

+  \item \code{\link{row_order,HeatmapList-method}}: get order of rows

+  \item \code{\link{column_order,HeatmapList-method}}: get order of columns

+  \item \code{\link{row_dend,HeatmapList-method}}: get row dendrograms

+  \item \code{\link{column_dend,HeatmapList-method}}: get column dendrograms

 }}

 \author{

 Zuguang Gu <z.gu@dkfz.de>

@@ -27,7 +27,7 @@ HeatmapAnnotation(df, name, col, na_col = "grey",

   \item{na_col}{color for \code{NA} values in simple annotations.}

   \item{annotation_legend_param}{a list which contains parameters for annotation legends}

   \item{show_legend}{whether show legend for each column in \code{df}.}

-  \item{...}{functions which define complex annotations. Values should be named arguments.}

+  \item{...}{functions which define complex annotations or vectors of simple annotation. Values should be named arguments.}

   \item{which}{are the annotations row annotations or column annotations?}

   \item{annotation_height}{height of each annotation if annotations are column annotations.}

   \item{annotation_width}{width of each annotation if annotations are row annotations.}

@@ -55,6 +55,8 @@ df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = HeatmapAnnotation(df = df)

 ha = HeatmapAnnotation(df = df, col = list(type = c("a" =  "red", "b" = "blue")))

+ha = HeatmapAnnotation(type = c("a", "a", "a", "b", "b", "b"), 

+    col = list(type = c("a" =  "red", "b" = "blue")))

 ha = HeatmapAnnotation(df = df, col = list(type = c("a" =  "red", "b" = "blue")), 

     which = "row")

@@ -55,7 +55,11 @@ The \code{\link{HeatmapList-class}} provides following methods:

 \itemize{

   \item \code{\link{draw,HeatmapList-method}}: draw the list of heatmaps and row annotations.

-  \item \code{\link{add_heatmap,HeatmapList-method}} add heatmaps to the list of heatmaps.

+  \item \code{\link{add_heatmap,HeatmapList-method}}: add heatmaps to the list of heatmaps.

+  \item \code{\link{row_order,HeatmapList-method}}: get order of rows

+  \item \code{\link{column_order,HeatmapList-method}}: get order of columns

+  \item \code{\link{row_dend,HeatmapList-method}}: get row dendrograms

+  \item \code{\link{column_dend,HeatmapList-method}}: get column dendrograms

 }}

 \author{

 Zuguang Gu <z.gu@dkfz.de>

@@ -34,7 +34,10 @@ A graphic function which can be set in \code{\link{HeatmapAnnotation}} construct

 Zuguang Gu <z.gu@dkfz.de>

 }

 \examples{

-# There is no example

-NULL

+mat = matrix(rnorm(10000), nr = 1000)

+labels = sample(letters, 20, replace = TRUE)

+Heatmap(mat, show_row_dend = FALSE, show_column_dend = FALSE) + 

+rowAnnotation(link = row_anno_link(at = sample(1000, 20), labels = labels),

+    width = unit(1, "cm") + max_text_width(labels))

 }

@@ -23,7 +23,7 @@ This function contructs the name of the viewport,

 goes to the viewport by \code{\link[grid]{seekViewport}} and applies code

 to that viewport.

-Since you know the number of leaves in the dendrogram, it is

+If you know the number of leaves in the dendrogram, it is

 simple to calculate the position of every leave in the dendrogram.

 E.g., for the column dendrogram, the i^th leave is located at:

@@ -23,7 +23,7 @@ This function contructs the name of the viewport,

 goes to the viewport by \code{\link[grid]{seekViewport}} and applies code

 to that viewport.

-Since you know the dimensions of the matrix, it is

+If you know the dimensions of the matrix, it is

 simple to calculate the position of every row name or column name in the heatmap.

 E.g., for the column column, the i^th name is located at:

@@ -22,7 +22,7 @@ This function contructs the name of the viewport,

 goes to the viewport by \code{\link[grid]{seekViewport}} and applies code

 to that viewport.

-Since you know the number of rows and columns for that row slice, it is

+If you know the number of rows and columns for that row slice, it is

 simple to calculate the position of every small grid in the row slice.

 E.g., the position for the grid in i^th row and j^th column is:

@@ -19,12 +19,12 @@ densityHeatmap(data,

 \arguments{

   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

-  \item{col}{a list of colors that density values are scaled to.}

+  \item{col}{a list of colors that density values are mapped to.}

   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame  and colors for annotations are randomly assigned. If you want to customize the annotation colors, use a \code{\link{HeatmapAnnotation-class}} object directly.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

+  \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -46,7 +46,8 @@ densityHeatmap(matrix)

 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))

 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))

-ha = HeatmapAnnotation(points = anno_points(runif(10)))

+ha = HeatmapAnnotation(points = anno_points(runif(10)),

+    anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))

 densityHeatmap(matrix, anno = ha)

 lt = list(rnorm(10), rnorm(10))

@@ -18,7 +18,7 @@ selectArea(mark = TRUE)

 Users can use mouse to click two positions on the heatmap, the function

 will return the row index and column index for the selected region in the selected matrix.

-Of cource this function only works under interactive graphical environment.

+This function only works under interactive graphical environment.

 }

 \value{

 A list containing row index and column index corresponding to the selected region.

@@ -33,4 +33,4 @@ to select a sub-area in the heatmap and retrieve index for rows and columns in t

 Since heatmaps are always used to visualize patterns that are clustered together, 

 this feature can greatly give convinience to extract the sub-matrix that users are interested in.

-<p><img src="select_region.gif" /></p>

+<p><img src="select_region.gif" width="600" /></p>

@@ -100,7 +100,7 @@ mat_list = unify_mat_list(mat_list)

 mat_list

 ```

-Same as the first example, but here we also define `background` in `alter_fun_list` argument. This function defines

+Same as the first example, but here we also define `background` in `alter_fun` argument. This function defines

 how to add graphics when there is no alteration and it is always put as the first in the list.

 ```{r}

@@ -133,7 +133,7 @@ oncoPrint(mat_list,

 ```

 If `alter_fun` is set as a single function, customization can be more flexible. In following example,

-rectangles always fill the whole grid.

+rectangles always fill the whole grid evenly.

 ```{r}

 oncoPrint(mat_list,

@@ -274,6 +274,10 @@ oncoPrint(mat, get_type = function(x) strsplit(x, ";")[[1]],

 	barplot_ignore = "AMP")

 ```

+If you make the plot in an interactive device (e.g. `X11` or Rstudio IDE), the generation of the plot

+may be very slow. In this case, we suggest users to directly save the plot to a separate file 

+(e.g. using `png()` or `pdf()`) and then visualize the plot afterwards.

+

 ## Session info