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NEWS
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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