NEWS

CHANGES in VERSION 2.11.1

* add a global option `ht_opt$COLOR` to control colors for continuous color mapping.
* `annotation_label` can be an `expression` object.
* `recycle_gp()`: now consider when n = 0.

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

CHANGES in VERSION 2.9.4

* fixed a bug of missing right annotation legends for vertically concatenated heatmaps.
* `Legend()`: support `border` to be set to `asis`.
* Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height).
* add a new argument `beside` in `anno_barplot()` to position bars beside each other.
* add `plot()` method for `Heatmap` and `HeatmapList` classes.
* add `anno_customize()`.

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

CHANGES in VERSION 2.9.3

* `pheatmap()`/`heatmap()`/`heatmap.2()`: set default of run_draw to FALSE.
* throw error when the heatmaps (list) are already initialized by draw() when adding them.
* set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects.
* `make_comb_mat()`: support `GRangesList` object as input.
* legends: fixed a bug of the grid heights were not correctedly calculated.
* discrete annotations: neighbour grids are merged into one single grid if they have the 
  same values.
* `anno_barplot()`: allows to add numbers on top of bars.
* `UpSet()`: axis labels are automatically formated for genomic coordinates.
* `AnnotationFunction()`: add a new argument `cell_fun`.
* When the dendrogram height is zero, the corresponding viewport has scale (0, 1).

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

CHANGES in VERSION 2.9.2

* fixed a bug of `bg_col` for transposed matrix in `UpSet()`.
* print warnings if names of annotations have different orders from the matrix row/column names.

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

CHANGES in VERSION 2.9.1

* fixed a bug of editing gTree object where the list element "just" has been 
  changed to "justification" in recent R versions.

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

CHANGES in VERSION 2.7.10

* `anno_simple()`: text symbols can have nchar > 1.
* `anno_text()`: add `show_name` argument.

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

CHANGES in VERSION 2.7.9

* add `frequencyHeatmap()`.
* add `Heatmap3D()`.

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

CHANGES in VERSION 2.7.8

* add `cluster_between_groups()`.
* add `graphics` argument in `anno_block()`.

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

CHANGES in VERSION 2.7.7

* discrete numeric legend labels are in correct order now.
* parallel is implemented with foreach + doParallel
* expression is properly processed for discrete legends
* `adjust_dend_by_x()`: simplified the representation of units.
* number of split can be the same as number of matrix rows/columns.

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

CHANGES in VERSION 2.7.6

* `Legend()`: add a new argument `grob`.

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

CHANGES in VERSION 2.7.5

* `anno_block()`: add `labels_offset` and `labels_just`.
* `anno_lines()`: `show_points` can be a vector.
* `pheatmap()`: support `kmeans_k`.

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

CHANGES in VERSION 2.7.4

* add `save_last` option in `ht_opt()`.

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

CHANGES in VERSION 2.7.1

* `normalize_comb_mat()`: add `full_comb_sets` and `complement_set` arguments to control
  full sets of combination sets.
* adjust the space of column title according to ggplot2.
* `Legend()`: for title_position == "lefttop", the title position is adjusted.
* Legends are automatically adjusted according to the device size when resizing the device.
* `Legend()`: add `interval_dist` to control the distance of two neighbouring breaks.
* Fixed a bug that it crashes Rstudio
* `make_comb_mat()`: print warning messages when there are NA values in the matrix.
* temporary solution for woking under retina display with Rstudio
* add `bin_genome()` and `normalize_genomic_signals_to_bins()`
* print messages if directly sending `anno_*()` functions to `top_annotation` or similar arguments.
* `pheatmap()`: set heatmap name to " " so that there is no legend title by default.
* also translate `stats::heatmap()` and `gplots::heatmap.2()`.
* move all code for interactive heatmap to InteractiveComplexHeatmap package.

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

CHANGES in VERSION 2.5.6

* `ht_shiny()`: add argument `app`.
* `grid.dendrogram()`: change the recursive implementation with iterations.
* change default raster device to `CairoPNG`.
* `Heatmap()`: If the discrete `col` covers more than the levels in the matrix,
  the full color set is still saved, which means, in `heatmap_legend_param` you 
  can set `at` that are not all in the matrix but are in the `col`.
* padding of the whole plot and spaces of column titles are adjusted to fit ggplot2 
* add `row_gap` and `column_gap` in `Legend()`.
* `oncoPrint()`: now draw legends the same as `alter_fun`.
* add a new function `attach_annotation()`.
* legends for row annotations can be grouped with column annotation legends.
* annotation name allows rotations.

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

CHANGES in VERSION 2.5.5

* still draw the legend when all values are NA in an annotation.
* add `show_fraction` argument in `anno_oncoprint_barplot()` function to show the fractions
  of mutations instead of the counts.
* `pheatmap()`: improve the setting of `color` and `breaks`.
* `ht_opt$TITLE_PADDING` can be set with a unit of length two.
* `HeatmapAnnotation()`: remove colors that are not in the annotations. 
* `pheatmap()`: fixed a bug when length(breaks) = length(color) + 1
* `pheatmap()`: legend breaks are centered to zero if the matrix is scaled.
* `pheatmap()`: color mapping is symmetric to zero when scale is set.
* support ragg package to write temporary png files
* `densityHeatmap()`: column dendrogram is reordered by column means for ks method.

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

CHANGES in VERSION 2.5.4

* fixed a bug where slice clusters were wrongly reordered.
* `Heatmap()`: add `border_gp` argument.
* Legends are nicely placed.
* `anno_block()`: allows to set height and width.
* support better rasterization.
* support setting graphics on dendrogram nodes.
* Add a new vignette "interactive heatmap"
* `Legends()`: fixed a bug of mixtype "legend" to "Legend".
* now assign correct envir to `decorate_dend()`.
* `pheatmap()`: check `NA` in the matrix.
* `grid.dendrogram()`: consider branches with height zero.
* checking the dimension of the matrix and the nobs of annotations when adding them.

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

CHANGES in VERSION 2.5.3

* add `selectArea()`/`selectPosition()` which allows interactively select a region from 
  the heatmaps.
* export the heatmap as a shiny app!!!
* `col` in `Heatmap()` accpets a `ColorMapping` object.
* `default_col()`: print a message if there are outliers in the matrix.
* `discrete_legend_body()`: adjust ncol and nrow if there are empty rows and columns in the layout.
* `anno_image()`: fixed a bug that images are not reordered.
* `anno_mark()`: now expression is correctly supported.
* `anno_zoom()`: order of index in `panel_fun` is adjusted to the order in the heatmap
* `list_to_matrix()`: convert elements to characters.
* print messages for `anno_mark()`, `anno_zoom()`, `draw_legend()` (if legends are wrapped) 
  if working under RStudio.

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

CHANGES in VERSION 2.5.2

* translate pheatmap to Heatmap
* `upset_top_annotation()` and `upset_right_annotation()`: the names of the annotations
   are changed to `intersection_size`, `set_size` and `union_size`.
* `list_components()`: adds `pattern` argument.

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

CHANGES in VERSION 2.5.1

* A temporary solution of the sum of two complicated units (in temp.R).

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

CHANGES in VERSION 2.3.4

* add `alter_graphic()` to automatically generate alteration graphic functions.
* add `label`/`annotation_label` argument in `SingleAnnotation()` and `HeatmapAnnotation()`.
* improved the subsetting methods for `comb_mat` class
* rewrite `smartAlign2()`

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

CHANGES in VERSION 2.3.3

* support **gridtext** package
* fixed the bug of node stack overflow when there are many identical rows for drawing the dendrogram.
  see (http://www.thinkingincrowd.me/2016/06/06/How-to-avoid-Stack-overflow-error-on-recursive/)
* support to set legend gaps
* print important messages, e.g. when number of rows are more than 2000, interanlly use_raster 
  is turned on and the message should be printed to users.
* UpSet plots: optimize the processing of many sets (current solution consumes huge memory)
* UpSet plots: the "intersect" and "union" modes are currectly calculated.
* `anno_block()`: add `show_name` argument.

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

CHANGES in VERSION 2.3.2

* `anno_simple()`: fixed a bug when pch are all NA in a slice
* adjust code according to grid 4.0.
* move scripts in test_not_run/ to tests/ folder
* `Heatmap()`: `cluster_row_slice`/`cluster_column_slice` set to TRUE
  by default for character matrix and when dendrogram is already provided.
* `smartAlign2()`: improved the code that positions are correctly calculated.
* row titles are in the correct order if they are set as "template".

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

CHANGES in VERSION 2.3.1

* `anno_points()`: allows images as symbols.
* add `HEATMAP_LEGEND_PADDING` and `ANNOTATION_LEGEND_PADDING` options in `ht_opt`
* `oncoPrint()`: print messages if there are NA values in the input matrix

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

CHANGES in VERSION 2.1.1

* `Heatmap()`: give error when heatmap has empty string as its name.
* `anno_mark()`: text positions are correctly calculated now with rotations.
* The order of legend labels are ordered by either `sort` or `levels`.

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

CHANGES in VERSION 2.1.0

* check the length of the clustering objects and the matrix rows/columns
* `anno_oncoprint_barplot()`: add `ylim` argumnet
* `anno_mark()`: add `labels_rot` argument
* `draw_legend()`: legends for annotations with the same names are merged
* `densityHeatmap()`: `ylim` works as it is expected.
* add `cluster_row_slices` and `cluster_column_slices` to `draw,HeatmapList-method()`
* `densityHeatmap()`: `col` can be set as a function
* add `cluster_rows`/`cluster_columns` in `oncoPrint()`
* legend labels support symbols
* `Heatmap()`: add `jitter` argument to add tiny random shift to original matrix. 
   It is mainly to solve the problem of "Error: node stack overflow"
   when there are too many identical rows/columns for plotting the dendrograms.

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

CHANGES in VERSION 1.99.8

* add `title_gap` in `Legend()
* fixed a bug of wrong row title spaces when multiple heatmaps are vertically
  concatenated.
* fixed a bug of *_sub_title_side when the heatmap annotation is the first/last
  element in the heatmap list.
* zero-column/row heatmap is supported.
* improved calculation of axis breaks

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

CHANGES in VERSION 1.99.7

* `UpSet()` supports adding complement sets.
* `make_comb_set()`: add `universal_set` and `complement_size` arguments.
* axes can be reversed in anno_* functions.

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

CHANGES in VERSION 1.99.6

* adjust the size of heatmap annotations and add testing scripts.
* run multiple times k-means to get a consensus partition.
* `show_heatmap_legend` is set to FALSE if `rect_gp = gpar(type = "none")`.
* add `restore_matrix()`.
* add `row_names_centered`/`column_names_centered` arguments to `Heatmap()`.
* `gp` in `anno_text()` supports `fill` and `border`.
* `Legend` adds boxplot-style legend.
* adjustment according to annotation extension is improved.

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

CHANGES in VERSION 1.99.5

* add `UpSet()` and some related functions to make Upset plots
* fixed bugs of drawing legends
* add `test_alter_fun()`
* `HeatmapAnnotation()`: fixed a bug for setting `height` when all annotations are simple annotations.
* `default_col()`: if the fraction of positive values in the matrix is in (0.3, 0.7), the color mapping
  is symmetric to zero.
* check `NA` values in `anno_boxplot()` and `anno_density()`.
* add `mc.cores` in `densityHeatmap()`.

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

CHANGES in VERSION 1.99.4

* anno_mark() is now calculated in multiple slices.
* oncoPrint(): automatically split the alteration type if the separator is one of ";:,|".
* add anno_zoom()

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

CHANGES in VERSION 1.99.1

* add `cluster_row_slices` and `cluster_column_slices` arguments in `Heatmap()`.
* 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.

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

CHANGES in VERSION 1.99.0

This a major update of the package. The main changes are:
* support column split
* support align heatmaps vertically
* add a naive `AnnotationFunction` class to handle annotation functions
* add more annotation functions

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

CHANGES in VERSION 1.19.1

* `Heatmap()`: no column name added if the input matrix is a one-column matrix.
* `oncoPrint()`: scales the the row annotations are now the same if rows are split.

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

CHANGES in VERSION 1.17.1

* `Legend()`: add `by_row` argument to control the arrangement of legends
  if they are put in more than one columns
* `Legend()`: use `textGrob()` if the point symbol is text
* `grid.dendrogram()`: fix a bug that the dendrogram is wrong when row/column
  names have duplicated names.
* `anno_boxplot()`: axis rescaled when outline = FALSE
* `oncoPrint()`: rows are first ordered by total number of mutations and then
  ordered by number of samples that have mutations
* correctly reorder rows
* add `row_gap` argument for list of heatmaps
* `oncoPrint()`: add `j` and `i` as optional argument for `alter_fun`

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

CHANGES in VERSION 1.15.1

* random colors are generated by new `rand_color()` function in circlize package.
* add `density_param` in `densityHeatmap()` function
* annotations with duplicated names have no legends any more
* re-implement `grid.xaxis()` to draw axis labels rotated 90 degrees
* grids in discrete legend are arranged by rows if ncol > 1
* raster image is generated in an independent R session
* empty string in annotation or heatmap is mapped to NA
* annotation and heatmap legends can be merged into one column. 
* change the default value of `row_names_max_width` and `column_names_max_height`
* default legend style for continuous values is changed to "continuous"
* add `grid.dendrogram2()` which draws dendrograms with uneven position for leaves
* move **dendextend** to Suggests field because it depends/imports rlang indirectly
  which has a `print.frame()` function and it will affect to print a `frame` object
  returned by `frameGrob()`.
* `decorate_*()` functions return to the viewport where they are called.
* fixed a bug that annotation names are drawn for all row slices.
* construct a valid path under Windows

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

CHANGES in VERSION 1.13.2

* add `packLegend()`

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

CHANGES in VERSION 1.13.1

* `Heatmap()`: add `km_title` to set the format of row title when `km` is set
* `anno_link()`: add `extend` to extend the regions for the labels
* `anno_boxplot()`: for row annotation, outliers are in the correct in y-axis.
  Thanks @gtg602c for the fix
* `HeatmapAnnotation()`: gaps are included in the size of the annotations
* `anno_link()`: graphic parameters are correctly reordered
* `densityHeatmap()`: viewport is created with `clip = TRUE`
* `decorate_*()`: add `envir` option to control where to look for variables inside `code`
* `Legend()`: title supports expression
* `anno_*()`: if the input is a data frame, warn that users may convert it to matrix

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

CHANGES in VERSION 1.11.8

* `anno_barplot()`: accept a matrix as input to plot stacked barplots

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

CHANGES in VERSION 1.11.7

* SingleAnnotation: if `col` is a vector with no names, it will be assigned
  as `level(value)` or `unique(value)`
* HeatmapAnnotation: give warnings if color is defined while with no annotations
* HeatmapAnnotation: check `col`, if it is not valid, give warnings
* catch error when making annotation graphics

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

CHANGES in VERSION 1.11.6

* simply bump the verison number
* `gap` in `Heatmap()` now can be a vector

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

CHANGES in VERSION 1.11.5

* `gap` in `HeatmapAnnotation` has been adjusted
* annotations support drawing names of either sides
* `densityHeatmap()`: quantile lines are also reordered
* export `anno_oncoprint_barplot`
* `Heatmap()`: if `col` is a unnamed vector and the number of colors is same as
  unique itemes in `mat`, the name of `col` vector is set to `sort(unique(mat))
* adjusted the order of annotation legends
* discreat legend: if a level is not in the data while defined by `col`, it will
  be removed.

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

CHANGES in VERSION 1.11.2

* `grid.dendrogram()`: do not draw dendrogram if the height is zero
* `densityHeatmap()`: support clustering on columns and more controls on column settings

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

CHANGES in VERSION 1.11.1

* `draw,HeatmapList-method` can control row order and clustering of the main heatmap

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

CHANGES in VERSION 1.9.7

* add `Legend()` function which is more flexible to generate
  different types of legends.

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

CHANGES in VERSION 1.9.6

* `color_mapping_legend()`, there are ticks on continuous color bar

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

CHANGES in VERSION 1.9.5

* add a section in the vignette to show how to adjust positions
  of column names when there are bottom annotations.
* fixed a bug that character NA values can not to assigned with na_col
* extra character 'at' and 'labels' in legends will be removed automatically
* all arguments which are passed to `make_layout()` are all explicitly put
  in `draw()` instead of using ...

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

CHANGES in VERSION 1.9.4

* heatmap bodied can be set as raster images if number of rows are too huge

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

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 supports adding graphics grid by grid
* add `show_pct` option in `oncoPrint()`
* add `column_order` in `densityHeatmap()`

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

CHANGES in VERSION 1.9.2

* imporved example of `anno_link()`

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

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
* add `anno_link()` annotation function
* bottom annotations are attached to the bottom edge of the heatmap 
  if there are additional blank space
* colors for NA can be set by "_NA_" in annotations
* `row_dend_reorder` and `column_dend_reorder` are set to `TRUE` by default again -_-!!
* optimize the way to specify na_col in heatmap annotations
* correct wrong viewport names in decorate_* functions

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

CHANGES in VERSION 1.7.3

* `oncoPrint()`: add `barplot_ignore` option to remove alterations
  that are not put on the barplot.
* `oncoPrint()`: delete extra alter_fun if they are not in the matrix

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

CHANGES in VERSION 1.7.2

* for `anno_points()`, `anno_barplot()`, `anno_boxplot()`, the name is assigned
  to the viewport with data ranges
* oncoPrint(): top_annotation is assigned with correct height

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

CHANGES in VERSION 1.7.1

* `x` and `y` are `unit` object now in `cell_fun`
* add an example to visualize GO game
* transparency is kept when making discreate color mappings
* `oncoPrint()`: barplots on top now are controlled by `top_annotation` argument

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

CHANGES in VERSION 1.5.1

* `oncoPrint`: there are default graphics if type of alterations is 
  less than two.
* `anno_*`: get rid of lazy loading

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

CHANGES in VERSION 1.4.4

* NULL can be added to the heatmap list
* give message if users mess up with row and column annotations
* `oncoPrint`: columns are sorted by `memo sort` method to enhance
  the mutual exclusivity.

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

CHANGES in VERSION 1.4.3

* `anno_boxplot`: outliers can correctly plotted
* add a new function `enhanced_basicplot`
* fix a bug that order of annotation height is reversed

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

CHANGES in VERSION 1.4.2

* order of annotations can be adjusted arbitrarily
* anno_barplot: scales are adjusted according to the baseline

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

CHANGES in VERSION 1.4.1

* revised the vignettes

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

CHANGES in VERSION 1.4.0

* returned value for `draw` method has been changes
* add `row_order`, `column_order`, `row_dend` and `column_dend`
  to extract orders and dendrograms after heatmap clustering
* add `select` function to interactively select sub region in the heatmap
  and retrieve row/column index in the selected sub region.
* renames all varialbes `*hclust*` to `*dend*`

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

CHANGES in VERSION 1.3.3

* set `row_reorder` and `column_reorder` to FALSE by default in `Heatmap()`

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

CHANGES in VERSION 1.3.2

* fixed the error in the vignette header

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

CHANGES in VERSION 1.3.1

* padding of whole plot are correctly set now

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

CHANGES in VERSION 1.3.0

* parameters for legend are specified by a list
* vignette was split into several vignettes which focus on specific topics
* ColorMapping class suppoorts `at` and `labels`
* add `row_anno_*` and `column_anno_*` functions
* `anno_barplot` add `baseline` option to define the baseline of bars
* change default colors for matrix
* allow heatmap with zero-row
* heatmap components can all have absolute units
* add `oncoPriint()`

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

CHANGES in VERSION 1.2.8

* add decorate* functions

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

CHANGES in VERSION 1.2.7

* add `rows_reorder_weight` and `columns_reorder_weight` in `Heatmap()`
* `draw,HeatmapList-method` returns a list of orders
* clustering is stored as dendrogram internally

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

CHANGES in VERSION 1.2.6

* graphical parameters for row names can be set as same length
  as row slices
* graphical parameters for annotation functions are consistent with
  the matrix now
* insert `k = NULL` into anno_function if they are row annotations
* add a new vignette "quick examples"
* change style for continuous legend color bar
* label order of discrete legend has been adjusted (now it is from top to bottom)

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

CHANGES in VERSION 1.2.5

* add dependency of base packages

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

CHANGES in VERSION 1.2.4

* name for ColorMapping object has default value now. 
* legend for continuous values can be set as continuous legends
* row title and column title as well as legend title support expression
* add `heatmap_legend_title` in `Heatmap` and `ColorMapping`
* fixed a bug in `plotDataFrame`

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

CHANGES in VERSION 1.2.3

* `color_mapping_legend` can produce a continuous color legend
* `color_mapping_legend` now returns a grob object

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

CHANGES in VERSION 1.2.2

* adjust positions for row titles
* rows can be split if `cluster_rows` are a clustering object
* `row_order` and `column_order` can be set by dimension names

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

CHANGES in VERSION 1.2.1

* adjust orders of row slices
* support text rotation for heatmap titles 

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

CHANGES in VERSION 1.2.0

* correct row orders if km and row_order is set in `Heatmap`

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

CHANGES in VERSION 1.1.9

* adjust names and size of each component
* add `densityHeatmap` function which visualizes column distribution
  in a matrix
* add `plotDataFrame` function which provides a quick way to 
  visualize a data frame

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

CHANGES in VERSION 1.1.8

* dendrograms are implemented by `grid.segments` 
* setting padding for each component
* adjust gaps between heatmaps/row annotations if the column of the 
  heatmap is zero.

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


CHANGES IN VERSION 1.1.7

* check consistency of matrix row names

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

CHANGES IN VERSION 1.1.6

* improved generation of random colors
* order of heatmap annotation legends are same as the order of annotations
* support NA value in simple annotations
* add examples in the vignette
* simple row annotations now have the correct order
* `col` can be a vector of colors if matrix is continuous
* simple annotation can be logical

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

CHANGES IN VERSION 1.1.5

* add gaps between heatmap components

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

CHANGES IN VERSION 1.1.4

* support color mapping for NA values

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

CHANGES IN VERSION 1.1.3

* Improved vignette to describe how to use row index in row annotation function
  if row annotations are also splitted by rows.

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

CHANGES IN VERSION 1.1.2

* `anno_density`: graphics are now in correct order
* add `anno_text`
* add new examples corresponding to new functions

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

CHANGES IN VERSION 1.1.1

* fixed a bug when setting `cluster_rows` to FALSE but still cluster
  on rows.
* add `rowAnnotation` and `columnAnnotation` functions
* add examples in the vignette
* No error if the heatmap list only contains zero-column matrix

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

CHANGES IN VERSION 0.99.2

* add two examples in vignette
* add chunk labels in the vignette

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

CHANGES IN VERSION 0.99.1

* x and y in `cell_fun` are now `unit` objects.

=================================================
CHANGES IN VERSION 0.99.0

* First release