NEWS

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

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

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