NEWS
5b47a845
 CHANGES in VERSION 2.3.2
 
 * support gridtext
7539e693
 * `anno_simple()`: fixed a bug when pch are all NA in a slice
5b47a845
 
 ========================
 
260b45a1
 CHANGES in VERSION 2.3.1
 
 * `anno_points()`: allows images as symbols.
1b0df470
 * add `HEATMAP_LEGEND_PADDING` and `ANNOTATION_LEGEND_PADDING` options in `ht_opt`
a867f462
 * `oncoPrint()`: print messages if there are NA values in the input matrix
260b45a1
 
 ========================
 
6e4e35c3
 CHANGES in VERSION 2.1.1
 
 * `Heatmap()`: give error when heatmap has empty string as its name.
7abc442a
 * `anno_mark()`: text positions are correctly calculated now with rotations.
d4061ead
 * The order of legend labels are ordered by either `sort` or `levels`.
6e4e35c3
 
 ========================
 
86907a77
 CHANGES in VERSION 2.1.0
 
 * check the length of the clustering objects and the matrix rows/columns
21a65de8
 * `anno_oncoprint_barplot()`: add `ylim` argumnet
f4dac009
 * `anno_mark()`: add `labels_rot` argument
3ebc7290
 * `draw_legend()`: legends for annotations with the same names are merged
85651335
 * `densityHeatmap()`: `ylim` works as it is expected.
bf60e9d4
 * add `cluster_row_slices` and `cluster_column_slices` to `draw,HeatmapList-method()`
ab596f42
 * `densityHeatmap()`: `col` can be set as a function
38cd0ae5
 * add `cluster_rows`/`cluster_columns` in `oncoPrint()`
0ea69256
 * legend labels support symbols
9e95ee32
 * `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.
86907a77
 
 ========================
 
062a0376
 CHANGES in VERSION 1.99.8
 
 * add `title_gap` in `Legend()
4e328f38
 * fixed a bug of wrong row title spaces when multiple heatmaps are vertically
   concatenated.
780489e4
 * 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.
69f9bed7
 * improved calculation of axis breaks
062a0376
 
 ========================
 
9e4037d8
 CHANGES in VERSION 1.99.7
 
 * `UpSet()` supports adding complement sets.
698e6611
 * `make_comb_set()`: add `universal_set` and `complement_size` arguments.
529f6dba
 * axes can be reversed in anno_* functions.
9e4037d8
 
 ========================
 
0c139e20
 CHANGES in VERSION 1.99.6
 
0d456ec7
 * 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.
0c139e20
 
 ========================
 
948414fa
 CHANGES in VERSION 1.99.5
 
 * add `UpSet()` and some related functions to make Upset plots
69345c7d
 * fixed bugs of drawing legends
79f19153
 * add `test_alter_fun()`
d90404d6
 * `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.
daedc41b
 * check `NA` values in `anno_boxplot()` and `anno_density()`.
13593e26
 * add `mc.cores` in `densityHeatmap()`.
948414fa
 
 ========================
fda8e6f1
 
138dc569
 CHANGES in VERSION 1.99.4
 
 * anno_mark() is now calculated in multiple slices.
fda8e6f1
 * oncoPrint(): automatically split the alteration type if the separator is one of ";:,|".
 * add anno_zoom()
138dc569
 
 ========================
 
5e6b381e
 CHANGES in VERSION 1.99.1
 
 * add `cluster_row_slices` and `cluster_column_slices` arguments in `Heatmap()`.
841f0bba
 * fixed a bug when annotation_height with only one annotation
a46b9f54
 * order of k-means slices are reordered by slice mean of `row_reorder`/`column_reorder`
   if they are provided as vectors.
1d6f282b
 * remove **rsvg** from Suggests.
5e6b381e
 
 =======================
 
6f11a271
 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
6f036283
 * add more annotation functions
6f11a271
 
 =======================
 
88137d23
 CHANGES in VERSION 1.19.1
 
 * `Heatmap()`: no column name added if the input matrix is a one-column matrix.
beeed537
 * `oncoPrint()`: scales the the row annotations are now the same if rows are split.
88137d23
 
 =======================
 
 CHANGES in VERSION 1.17.1
b7016a65
 
 * `Legend()`: add `by_row` argument to control the arrangement of legends
   if they are put in more than one columns
c7d95bdc
 * `Legend()`: use `textGrob()` if the point symbol is text
1451d75a
 * `grid.dendrogram()`: fix a bug that the dendrogram is wrong when row/column
   names have duplicated names.
ff0ecd4e
 * `anno_boxplot()`: axis rescaled when outline = FALSE
1422ff8d
 * `oncoPrint()`: rows are first ordered by total number of mutations and then
   ordered by number of samples that have mutations
65b93c4d
 * correctly reorder rows
f987141a
 * add `row_gap` argument for list of heatmaps
ddf13e44
 * `oncoPrint()`: add `j` and `i` as optional argument for `alter_fun`
b7016a65
 
 =======================
 
2b4f31da
 CHANGES in VERSION 1.15.1
 
 * random colors are generated by new `rand_color()` function in circlize package.
eaef1222
 * 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
9487d939
 * grids in discrete legend are arranged by rows if ncol > 1
0623db7b
 * raster image is generated in an independent R session
9487d939
 * empty string in annotation or heatmap is mapped to NA
 * annotation and heatmap legends can be merged into one column. 
b502007d
 * change the default value of `row_names_max_width` and `column_names_max_height`
0623db7b
 * 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.
3c3ed664
 * fixed a bug that annotation names are drawn for all row slices.
6b6db389
 * construct a valid path under Windows
eaef1222
 
9487d939
 =======================
2b4f31da
 
c0659b22
 CHANGES in VERSION 1.13.2
 
 * add `packLegend()`
 
 ========================
 
b93ffad7
 CHANGES in VERSION 1.13.1
 
 * `Heatmap()`: add `km_title` to set the format of row title when `km` is set
e35e3579
 * `anno_link()`: add `extend` to extend the regions for the labels
765c7893
 * `anno_boxplot()`: for row annotation, outliers are in the correct in y-axis.
   Thanks @gtg602c for the fix
7b168003
 * `HeatmapAnnotation()`: gaps are included in the size of the annotations
18a667c5
 * `anno_link()`: graphic parameters are correctly reordered
8189a4cf
 * `densityHeatmap()`: viewport is created with `clip = TRUE`
d240a4c0
 * `decorate_*()`: add `envir` option to control where to look for variables inside `code`
1b1ae7f1
 * `Legend()`: title supports expression
04b77a1b
 * `anno_*()`: if the input is a data frame, warn that users may convert it to matrix
7b168003
 
b93ffad7
 ========================
 
02998f61
 CHANGES in VERSION 1.11.8
 
 * `anno_barplot()`: accept a matrix as input to plot stacked barplots
 
 =========================
 
71fd0acc
 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)`
57aebadf
 * HeatmapAnnotation: give warnings if color is defined while with no annotations
1498834c
 * HeatmapAnnotation: check `col`, if it is not valid, give warnings
fcaccd8a
 * catch error when making annotation graphics
71fd0acc
 
 ==========================
 
a0f802cb
 CHANGES in VERSION 1.11.6
 
 * simply bump the verison number
4b584cc3
 * `gap` in `Heatmap()` now can be a vector
 
 ===========================
a0f802cb
 
5b59131c
 CHANGES in VERSION 1.11.5
 
 * `gap` in `HeatmapAnnotation` has been adjusted
4684fe02
 * annotations support drawing names of either sides
3498de54
 * `densityHeatmap()`: quantile lines are also reordered
0286e386
 * export `anno_oncoprint_barplot`
8f2031d2
 * `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))
da23e9aa
 * adjusted the order of annotation legends
 * discreat legend: if a level is not in the data while defined by `col`, it will
   be removed.
5b59131c
 
 =============================
 
9cc6c383
 CHANGES in VERSION 1.11.2
 
be7413e1
 * `grid.dendrogram()`: do not draw dendrogram if the height is zero
9cc6c383
 * `densityHeatmap()`: support clustering on columns and more controls on column settings
 
 =============================
 
55b56e3d
 CHANGES in VERSION 1.11.1
 
 * `draw,HeatmapList-method` can control row order and clustering of the main heatmap
 
 =============================
 
d1359159
 CHANGES in VERSION 1.9.7
 
 * add `Legend()` function which is more flexible to generate
   different types of legends.
 
 ============================
 
ca09c9ba
 CHANGES in VERSION 1.9.6
 
 * `color_mapping_legend()`, there are ticks on continuous color bar
 
 =============================
 
fc0d2b3e
 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.
368bfc48
 * fixed a bug that character NA values can not to assigned with na_col
4c449c56
 * extra character 'at' and 'labels' in legends will be removed automatically
dc49bda8
 * all arguments which are passed to `make_layout()` are all explicitly put
   in `draw()` instead of using ...
fc0d2b3e
 
 =============================
 
2a78c184
 CHANGES in VERSION 1.9.4
 
 * heatmap bodied can be set as raster images if number of rows are too huge
 
 ==============================
 
21ca48b4
 CHANGES in VERSION 1.9.3
9f693eb5
 
 * graphic parameters are correctly recycled in row annotations
fdad789d
 * if there is only one row after splitting, there will be no dendrogram
d18549f4
 * add `range` option in `densityHeatmap()`
4b1b09fe
 * when `gap` is set for the main heatmap, other heatmps also adjust their `gap` values to it
7cc2d739
 * fixed a bug that when rownames/colnames are not complete, dendrograms are corrupted
21ca48b4
 * `alter_fun` now supports adding graphics grid by grid
6d8c4ef4
 * add `show_pct` option in `oncoPrint()`
7cd2ea7d
 * add `column_order` in `densityHeatmap()`
9f693eb5
 
 ==============================
 
21ca48b4
 CHANGES in VERSION 1.9.2
b42b69eb
 
 * imporved example of `anno_link()`
 
 ==============================
 
21ca48b4
 CHANGES in VERSION 1.9.1
eac1eca7
 
 * 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
44425cfd
 * bottom annotations are attached to the bottom edge of the heatmap 
   if there are additional blank space
2297ba87
 * colors for NA can be set by "_NA_" in annotations
7b914edf
 * `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
eac1eca7
 
 ===============================
 
e46e583b
 CHANGES in VERSION 1.7.3
 
 * `oncoPrint()`: add `barplot_ignore` option to remove alterations
   that are not put on the barplot.
83ef8139
 * `oncoPrint()`: delete extra alter_fun if they are not in the matrix
e46e583b
 
eac1eca7
 ================================
 
69869b05
 CHANGES in VERSION 1.7.2
 
 * for `anno_points()`, `anno_barplot()`, `anno_boxplot()`, the name is assigned
   to the viewport with data ranges
e46e583b
 * oncoPrint(): top_annotation is assigned with correct height
69869b05
 
 ===============================
 
44edc392
 CHANGES in VERSION 1.7.1
 
 * `x` and `y` are `unit` object now in `cell_fun`
 * add an example to visualize GO game
0ef1758b
 * transparency is kept when making discreate color mappings
bb8e309c
 * `oncoPrint()`: barplots on top now are controlled by `top_annotation` argument
44edc392
 
 ================================
 
5705ac14
 CHANGES in VERSION 1.5.1
 
 * `oncoPrint`: there are default graphics if type of alterations is 
   less than two.
e9b27b44
 * `anno_*`: get rid of lazy loading
5705ac14
 
 =================================
 
5c37ff0a
 CHANGES in VERSION 1.4.4
 
 * NULL can be added to the heatmap list
fd216ead
 * give message if users mess up with row and column annotations
dfa0170a
 * `oncoPrint`: columns are sorted by `memo sort` method to enhance
   the mutual exclusivity.
5c37ff0a
 
 ==================================
 
e6580410
 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
 
 ===================================
 
691842c7
 CHANGES in VERSION 1.4.2
 
5eb00348
 * order of annotations can be adjusted arbitrarily
691842c7
 * anno_barplot: scales are adjusted according to the baseline
 
 ===================================
 
e0b7d4e2
 CHANGES in VERSION 1.4.1
 
 * revised the vignettes
 
 ===================================
 
455d2853
 CHANGES in VERSION 1.4.0
bb5445cb
 
 * 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
455d2853
 * add `select` function to interactively select sub region in the heatmap
bb5445cb
   and retrieve row/column index in the selected sub region.
455d2853
 * renames all varialbes `*hclust*` to `*dend*`
bb5445cb
 
 ====================================
 
17db1ac5
 CHANGES in VERSION 1.3.3
 
 * set `row_reorder` and `column_reorder` to FALSE by default in `Heatmap()`
 
 =====================================
 
2b02a533
 CHANGES in VERSION 1.3.2
 
 * fixed the error in the vignette header
 
 ======================================
 
7f461366
 CHANGES in VERSION 1.3.1
 
 * padding of whole plot are correctly set now
 
 =======================================
 
262e3960
 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
50e388af
 * change default colors for matrix
41176f68
 * allow heatmap with zero-row
 * heatmap components can all have absolute units
25191b4d
 * add `oncoPriint()`
262e3960
 
 =========================================
 
3429d282
 CHANGES in VERSION 1.2.8
 
 * add decorate* functions
 
 =========================================
 
d5adc92b
 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
 
 =========================================
 
5382e69b
 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"
fa1ce092
 * change style for continuous legend color bar
5ad45803
 * label order of discrete legend has been adjusted (now it is from top to bottom)
5382e69b
 
 =========================================
 
271d0190
 CHANGES in VERSION 1.2.5
 
 * add dependency of base packages
 
 =========================================
 
e811f810
 CHANGES in VERSION 1.2.4
 
b1fe0a94
 * name for ColorMapping object has default value now. 
ff9ffa81
 * 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`
0dd34f1e
 * fixed a bug in `plotDataFrame`
e811f810
 
 ==========================================
 
2ac3bebe
 CHANGES in VERSION 1.2.3
 
fe00b614
 * `color_mapping_legend` can produce a continuous color legend
2ac3bebe
 * `color_mapping_legend` now returns a grob object
 
 ===========================================
 
a61c1013
 CHANGES in VERSION 1.2.2
 
dbcd94f0
 * adjust positions for row titles
a61c1013
 * rows can be split if `cluster_rows` are a clustering object
 * `row_order` and `column_order` can be set by dimension names
 
 ===========================================
 
a2746399
 CHANGES in VERSION 1.2.1
 
 * adjust orders of row slices
 * support text rotation for heatmap titles 
 
 ===========================================
 
d78f0496
 CHANGES in VERSION 1.2.0
 
 * correct row orders if km and row_order is set in `Heatmap`
 
 ===========================================
 
7a90e914
 CHANGES in VERSION 1.1.9
 
4769a516
 * adjust names and size of each component
91a200fd
 * add `densityHeatmap` function which visualizes column distribution
   in a matrix
7a90e914
 * add `plotDataFrame` function which provides a quick way to 
   visualize a data frame
 
 ============================================
 
a1bbefcc
 CHANGES in VERSION 1.1.8
 
 * dendrograms are implemented by `grid.segments` 
7cec59e4
 * setting padding for each component
 * adjust gaps between heatmaps/row annotations if the column of the 
   heatmap is zero.
a1bbefcc
 
 ============================================
 
 
ca391411
 CHANGES IN VERSION 1.1.7
 
 * check consistency of matrix row names
 
 =============================================
 
43617422
 CHANGES IN VERSION 1.1.6
9b297dee
 
43617422
 * improved generation of random colors
 * order of heatmap annotation legends are same as the order of annotations
9b297dee
 * support NA value in simple annotations
d4e46e73
 * 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
9b297dee
 
43617422
 ==============================================
 
 CHANGES IN VERSION 1.1.5
 
 * add gaps between heatmap components
 
9b297dee
 ===============================================
 
102bd01c
 CHANGES IN VERSION 1.1.4
 
 * support color mapping for NA values
 
 ===============================================
 
0cc581f9
 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.
 
 ===============================================
 
ff9378c4
 CHANGES IN VERSION 1.1.2
 
 * `anno_density`: graphics are now in correct order
 * add `anno_text`
 * add new examples corresponding to new functions
 
 ================================================
 
6811bed2
 CHANGES IN VERSION 1.1.1
f007215d
 
 * fixed a bug when setting `cluster_rows` to FALSE but still cluster
   on rows.
2fd8ba9a
 * add `rowAnnotation` and `columnAnnotation` functions
 * add examples in the vignette
 * No error if the heatmap list only contains zero-column matrix
 
 =================================================
f007215d
 
a2b2fe8d
 CHANGES IN VERSION 0.99.2
 
908b32ee
 * add two examples in vignette
a2b2fe8d
 * add chunk labels in the vignette
 
 =================================================
 
c753e552
 CHANGES IN VERSION 0.99.1
 
 * x and y in `cell_fun` are now `unit` objects.
 
 =================================================
 CHANGES IN VERSION 0.99.0
a83257df
 
 * First release