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fixed a bug where size of column titles was wrongly calculated

Zuguang Gu authored on 27/10/2022 09:23:08
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@@ -2,6 +2,7 @@ CHANGES in VERSION 2.13.4
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 * `anno_barplot()`: fixed a bug when split is set, the bars are wrongly plotted under besides = TRUE.
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 * `anno_boxplot()`: add two new argumetn: `add_points` and `pt_gp`.
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+* fixed a bug of size of column title wrongly calculated.
5 6
 
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 ========================
7 8
 
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add a new add_points argument in anno_boxplot()

Zuguang Gu authored on 27/10/2022 08:59:57
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 CHANGES in VERSION 2.13.4
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3 3
 * `anno_barplot()`: fixed a bug when split is set, the bars are wrongly plotted under besides = TRUE.
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+* `anno_boxplot()`: add two new argumetn: `add_points` and `pt_gp`.
4 5
 
5 6
 ========================
6 7
 
Browse code

anno_barplot(): fixed a bug when besides = TRUE

Zuguang Gu authored on 27/10/2022 08:33:37
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+CHANGES in VERSION 2.13.4
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+
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+* `anno_barplot()`: fixed a bug when split is set, the bars are wrongly plotted under besides = TRUE.
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+
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+========================
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+
1 7
 CHANGES in VERSION 2.13.2
2 8
 
3 9
 * `HeatmapAnnotation()`: fixed a bug where annotation legends are not all generated when `df` is set.
Browse code

anno_density(): fixed a bug where 'xlim' is ignored for 'heatmap'

Zuguang Gu authored on 28/09/2022 13:59:00
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@@ -3,6 +3,7 @@ CHANGES in VERSION 2.13.2
3 3
 * `HeatmapAnnotation()`: fixed a bug where annotation legends are not all generated when `df` is set.
4 4
 * `UpSet()`: now `bg_col` can be a vector of length more than two.
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 * `oncoPrint()`: Add `pct_include` argument.
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+* `anno_density()`: fixed a bug where `xlim` is ignored for "heatmap".
6 7
 
7 8
 ========================
8 9
 
Browse code

add pct_include argument

Zuguang Gu authored on 02/09/2022 07:57:24
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@@ -2,6 +2,7 @@ CHANGES in VERSION 2.13.2
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3 3
 * `HeatmapAnnotation()`: fixed a bug where annotation legends are not all generated when `df` is set.
4 4
 * `UpSet()`: now `bg_col` can be a vector of length more than two.
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+* `oncoPrint()`: Add `pct_include` argument.
5 6
 
6 7
 ========================
7 8
 
Browse code

bg_col can be set to a vector of length more than two

Zuguang Gu authored on 01/09/2022 19:33:43
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1 1
 CHANGES in VERSION 2.13.2
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3 3
 * `HeatmapAnnotation()`: fixed a bug where annotation legends are not all generated when `df` is set.
4
+* `UpSet()`: now `bg_col` can be a vector of length more than two.
4 5
 
5 6
 ========================
6 7
 
Browse code

fixed a bug of annotation legens when 'df' is set

Zuguang Gu authored on 31/08/2022 14:37:52
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+CHANGES in VERSION 2.13.2
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+
3
+* `HeatmapAnnotation()`: fixed a bug where annotation legends are not all generated when `df` is set.
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+
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+========================
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+
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 CHANGES in VERSION 2.13.1
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3 9
 * `column_title_rot` can be set with any degree value.
Browse code

comb_col is now correctly assigned when the combination matrix is transposed

Zuguang Gu authored on 27/07/2022 09:51:25
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@@ -2,6 +2,7 @@ CHANGES in VERSION 2.13.1
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 * `column_title_rot` can be set with any degree value.
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 * automatically recognize Jupyter environment.
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+* `UpSet()`: `comb_col` now is correctly assigned when the combination matrix is transposed.
5 6
 
6 7
 ========================
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Browse code

use foreach

Zuguang Gu authored on 31/05/2022 13:27:23
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 CHANGES in VERSION 2.13.1
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 * `column_title_rot` can be set with any degree value.
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+* automatically recognize Jupyter environment.
4 5
 
5 6
 ========================
6 7
 
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column_title_rot can be any degree value

Zuguang Gu authored on 31/05/2022 09:48:27
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+CHANGES in VERSION 2.13.1
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+
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+* `column_title_rot` can be set with any degree value.
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+
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+========================
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+
1 7
 CHANGES in VERSION 2.11.2
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 * discrete color mapping: when heatmap_param_list$at is set, it is reduced accordingly 
Browse code

reduce at and label for heatmap_legend_param according to col

Zuguang Gu authored on 12/04/2022 16:11:28
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+CHANGES in VERSION 2.11.2
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+
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+* discrete color mapping: when heatmap_param_list$at is set, it is reduced accordingly 
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+  to `col`.
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+
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+=======================
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+
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 CHANGES in VERSION 2.11.1
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 * add a global option `ht_opt$COLOR` to control colors for continuous color mapping.
Browse code

global variables in cell_fun are automatically saved

Zuguang Gu authored on 02/04/2022 15:52:11
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@@ -8,6 +8,8 @@ CHANGES in VERSION 2.11.1
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 * add `show_name` argument in `anno_empty()`.
9 9
 * the validation of annotations in `HeatmapAnnotation()` is simplified.
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 * add `anno_numeric()`.
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+* when `rect_gp = gpar(type = "none")`, `use_raster` is enforced to be FALSE.
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+* "global variables" outside `cell_fun`/`layer_fun` are aotumatially identified and saved locally.
11 13
 
12 14
 =========================
13 15
 
Browse code

add more annotation functions

Zuguang Gu authored on 18/02/2022 19:51:49
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@@ -6,6 +6,8 @@ CHANGES in VERSION 2.11.1
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 * `anno_block()`: add `align_to` argument.
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 * add `anno_text_box()` and `grid.text_box()`.
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 * add `show_name` argument in `anno_empty()`.
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+* the validation of annotations in `HeatmapAnnotation()` is simplified.
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+* add `anno_numeric()`.
9 11
 
10 12
 =========================
11 13
 
Browse code

add show_name in anno_empty()

Zuguang Gu authored on 03/02/2022 09:53:48
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@@ -3,6 +3,9 @@ CHANGES in VERSION 2.11.1
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 * add a global option `ht_opt$COLOR` to control colors for continuous color mapping.
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 * `annotation_label` can be an `expression` object.
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 * `recycle_gp()`: now consider when n = 0.
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+* `anno_block()`: add `align_to` argument.
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+* add `anno_text_box()` and `grid.text_box()`.
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+* add `show_name` argument in `anno_empty()`.
6 9
 
7 10
 =========================
8 11
 
Browse code

recycle_gp(): now consider n = 0

Zuguang Gu authored on 13/11/2021 10:42:20
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@@ -2,6 +2,7 @@ CHANGES in VERSION 2.11.1
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3 3
 * add a global option `ht_opt$COLOR` to control colors for continuous color mapping.
4 4
 * `annotation_label` can be an `expression` object.
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+* `recycle_gp()`: now consider when n = 0.
5 6
 
6 7
 =========================
7 8
 
Browse code

annotation_label accepts expression objects

Zuguang Gu authored on 08/11/2021 18:36:48
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 CHANGES in VERSION 2.11.1
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3 3
 * add a global option `ht_opt$COLOR` to control colors for continuous color mapping.
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+* `annotation_label` can be an `expression` object.
4 5
 
5 6
 =========================
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Browse code

add a new COLOR global option

Zuguang Gu authored on 08/11/2021 12:27:29
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+CHANGES in VERSION 2.11.1
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+
3
+* add a global option `ht_opt$COLOR` to control colors for continuous color mapping.
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+
5
+=========================
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+
1 7
 CHANGES in VERSION 2.9.4
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 * fixed a bug of missing right annotation legends for vertically concatenated heatmaps.
Browse code

update

Zuguang Gu authored on 25/10/2021 10:18:45
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@@ -5,6 +5,7 @@ CHANGES in VERSION 2.9.4
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 * Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height).
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 * add a new argument `beside` in `anno_barplot()` to position bars beside each other.
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 * add `plot()` method for `Heatmap` and `HeatmapList` classes.
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+* add `anno_customize()`.
8 9
 
9 10
 ========================
10 11
 
Browse code

add plot() method

Zuguang Gu authored on 29/09/2021 08:38:35
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@@ -4,6 +4,7 @@ CHANGES in VERSION 2.9.4
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 * `Legend()`: support `border` to be set to `asis`.
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 * Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height).
6 6
 * add a new argument `beside` in `anno_barplot()` to position bars beside each other.
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+* add `plot()` method for `Heatmap` and `HeatmapList` classes.
7 8
 
8 9
 ========================
9 10
 
Browse code

add new argument 'beside' in 'anno_barplot()'

Zuguang Gu authored on 28/09/2021 11:13:16
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@@ -3,6 +3,7 @@ CHANGES in VERSION 2.9.4
3 3
 * fixed a bug of missing right annotation legends for vertically concatenated heatmaps.
4 4
 * `Legend()`: support `border` to be set to `asis`.
5 5
 * Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height).
6
+* add a new argument `beside` in `anno_barplot()` to position bars beside each other.
6 7
 
7 8
 ========================
8 9
 
Browse code

restrict the size of the temp raster image

Zuguang Gu authored on 28/09/2021 09:20:28
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 CHANGES in VERSION 2.9.4
2 2
 
3 3
 * fixed a bug of missing right annotation legends for vertically concatenated heatmaps.
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+* `Legend()`: support `border` to be set to `asis`.
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+* Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height).
4 6
 
5 7
 ========================
6 8
 
Browse code

fixed a bug of missing right annotation legends for vertically concatenated heatmaps

Zuguang Gu authored on 09/09/2021 11:56:42
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 CHANGES in VERSION 2.9.4
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+* fixed a bug of missing right annotation legends for vertically concatenated heatmaps.
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+
3 5
 ========================
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 CHANGES in VERSION 2.9.3
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update

Zuguang Gu authored on 08/09/2021 13:02:52
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+CHANGES in VERSION 2.9.4
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+
3
+========================
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+
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 CHANGES in VERSION 2.9.3
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 * `pheatmap()`/`heatmap()`/`heatmap.2()`: set default of run_draw to FALSE.
Browse code

set max scale to 1 when dendrogram height is zero

Zuguang Gu authored on 08/09/2021 08:28:57
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@@ -10,6 +10,7 @@ CHANGES in VERSION 2.9.3
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 * `anno_barplot()`: allows to add numbers on top of bars.
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 * `UpSet()`: axis labels are automatically formated for genomic coordinates.
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 * `AnnotationFunction()`: add a new argument `cell_fun`.
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+* When the dendrogram height is zero, the corresponding viewport has scale (0, 1).
13 14
 
14 15
 =========================
15 16
 
Browse code

add a new argument cell_fun in AnnotationFunction()

Zuguang Gu authored on 04/08/2021 08:55:06
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   same values.
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 * `anno_barplot()`: allows to add numbers on top of bars.
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 * `UpSet()`: axis labels are automatically formated for genomic coordinates.
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+* `AnnotationFunction()`: add a new argument `cell_fun`.
12 13
 
13 14
 =========================
14 15
 
Browse code

axis labels are automatical formatted for genomic coordinates

Zuguang Gu authored on 03/08/2021 21:05:45
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@@ -8,6 +8,7 @@ CHANGES in VERSION 2.9.3
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 * discrete annotations: neighbour grids are merged into one single grid if they have the 
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   same values.
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 * `anno_barplot()`: allows to add numbers on top of bars.
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+* `UpSet()`: axis labels are automatically formated for genomic coordinates.
11 12
 
12 13
 =========================
13 14
 
Browse code

add numbers to the barplot annotations

Zuguang Gu authored on 03/08/2021 12:22:45
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@@ -7,6 +7,7 @@ CHANGES in VERSION 2.9.3
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 * legends: fixed a bug of the grid heights were not correctedly calculated.
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 * discrete annotations: neighbour grids are merged into one single grid if they have the 
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   same values.
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+* `anno_barplot()`: allows to add numbers on top of bars.
10 11
 
11 12
 =========================
12 13
 
Browse code

neighbour annotation grids are merged if they have the same value

Zuguang Gu authored on 03/08/2021 08:49:11
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 * set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects.
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 * `make_comb_mat()`: support `GRangesList` object as input.
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 * legends: fixed a bug of the grid heights were not correctedly calculated.
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+* discrete annotations: neighbour grids are merged into one single grid if they have the 
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+  same values.
8 10
 
9 11
 =========================
10 12
 
Browse code

fixed a bug of legend grids were not correctly recycled

Zuguang Gu authored on 02/08/2021 19:42:49
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@@ -4,6 +4,7 @@ CHANGES in VERSION 2.9.3
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 * throw error when the heatmaps (list) are already initialized by draw() when adding them.
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 * set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects.
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 * `make_comb_mat()`: support `GRangesList` object as input.
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+* legends: fixed a bug of the grid heights were not correctedly calculated.
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8 9
 =========================
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support GRangesList objects in make_comb_mat

Zuguang Gu authored on 02/08/2021 10:26:51
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 * `pheatmap()`/`heatmap()`/`heatmap.2()`: set default of run_draw to FALSE.
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 * throw error when the heatmaps (list) are already initialized by draw() when adding them.
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 * set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects.
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+* `make_comb_mat()`: support `GRangesList` object as input.
6 7
 
7 8
 =========================
8 9
 
Browse code

set wrap = TRUE when using grid.grabExpr()

Zuguang Gu authored on 26/07/2021 09:27:34
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 * `pheatmap()`/`heatmap()`/`heatmap.2()`: set default of run_draw to FALSE.
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 * throw error when the heatmaps (list) are already initialized by draw() when adding them.
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+* set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects.
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 =========================
7 8
 
Browse code

pheatmap do not call draw by default

Zuguang Gu authored on 22/07/2021 20:35:41
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+CHANGES in VERSION 2.9.3
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+
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+* `pheatmap()`/`heatmap()`/`heatmap.2()`: set default of run_draw to FALSE.
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+* throw error when the heatmaps (list) are already initialized by draw() when adding them.
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+
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+=========================
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+
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 CHANGES in VERSION 2.9.2
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 * fixed a bug of `bg_col` for transposed matrix in `UpSet()`.
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 * print warnings if names of annotations have different orders from the matrix row/column names.
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+=========================
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+
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 CHANGES in VERSION 2.9.1
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 * fixed a bug of editing gTree object where the list element "just" has been 
Browse code

check dimension names of matrices and annotations

Zuguang Gu authored on 13/07/2021 15:43:05
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 CHANGES in VERSION 2.9.2
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 * fixed a bug of `bg_col` for transposed matrix in `UpSet()`.
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+* print warnings if names of annotations have different orders from the matrix row/column names.
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 CHANGES in VERSION 2.9.1
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Browse code

add rmarkdown to Suggests

Zuguang Gu authored on 03/07/2021 08:17:56
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+CHANGES in VERSION 2.9.2
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+
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+* fixed a bug of `bg_col` for transposed matrix in `UpSet()`.
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+
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 CHANGES in VERSION 2.9.1
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 * fixed a bug of editing gTree object where the list element "just" has been 
Browse code

use github action

Zuguang Gu authored on 01/07/2021 11:29:17
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@@ -1,3 +1,10 @@
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+CHANGES in VERSION 2.9.1
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+
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+* fixed a bug of editing gTree object where the list element "just" has been 
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+  changed to "justification" in recent R versions.
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+
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+=========================
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+
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 CHANGES in VERSION 2.7.10
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 * `anno_simple()`: text symbols can have nchar > 1.
Browse code

version bump

Zuguang authored on 04/05/2021 13:55:58
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 * add `cluster_between_groups()`.
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 * add `graphics` argument in `anno_block()`.
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+=========================
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+
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 CHANGES in VERSION 2.7.7
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 * discrete numeric legend labels are in correct order now.
Browse code

add show_name argument in anno_text()

Zuguang authored on 07/04/2021 08:47:30
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 CHANGES in VERSION 2.7.10
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 * `anno_simple()`: text symbols can have nchar > 1.
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+* `anno_text()`: add `show_name` argument.
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 =========================
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anno_simple(): text symbol can have nchar > 1

Zuguang authored on 07/04/2021 08:20:24
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 CHANGES in VERSION 2.7.10
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+* `anno_simple()`: text symbols can have nchar > 1.
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+
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 =========================
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 CHANGES in VERSION 2.7.9
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increase version number

Zuguang authored on 04/04/2021 13:30:00
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+CHANGES in VERSION 2.7.10
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+
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+=========================
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+
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 CHANGES in VERSION 2.7.9
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 * add `frequencyHeatmap()`.
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add Heatmap3d()

Zuguang authored on 24/03/2021 09:05:20
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+CHANGES in VERSION 2.7.9
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+
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+* add `frequencyHeatmap()`.
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+* add `Heatmap3D()`.
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+
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+=========================
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+
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 CHANGES in VERSION 2.7.8
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 * add `cluster_between_groups()`.
Browse code

add 'graphics' argument in 'anno_block()'

Zuguang Gu authored on 11/03/2021 09:41:22
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 CHANGES in VERSION 2.7.8
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 * add `cluster_between_groups()`.
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+* add `graphics` argument in `anno_block()`.
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 CHANGES in VERSION 2.7.7
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add cluster_between_groups()

Zuguang Gu authored on 04/03/2021 09:51:27
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+CHANGES in VERSION 2.7.8
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+
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+* add `cluster_between_groups()`.
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+
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 CHANGES in VERSION 2.7.7
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 * discrete numeric legend labels are in correct order now.
Browse code

update docs

Zuguang Gu authored on 09/02/2021 20:31:08
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@@ -4,6 +4,7 @@ CHANGES in VERSION 2.7.7
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 * parallel is implemented with foreach + doParallel
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 * expression is properly processed for discrete legends
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 * `adjust_dend_by_x()`: simplified the representation of units.
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+* number of split can be the same as number of matrix rows/columns.
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 ==========================
9 10
 
Browse code

adjust_dend_by_x(): simplified the representation of units

Zuguang Gu authored on 09/02/2021 19:57:24
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@@ -3,6 +3,7 @@ CHANGES in VERSION 2.7.7
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 * discrete numeric legend labels are in correct order now.
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 * parallel is implemented with foreach + doParallel
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 * expression is properly processed for discrete legends
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+* `adjust_dend_by_x()`: simplified the representation of units.
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7 8
 ==========================
8 9
 
Browse code

expression is properly processed for discrete legends

Zuguang Gu authored on 09/02/2021 13:53:11
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-CHANGES in VERSION 2.7.5
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+CHANGES in VERSION 2.7.7
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 * discrete numeric legend labels are in correct order now.
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+* parallel is implemented with foreach + doParallel
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+* expression is properly processed for discrete legends
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5 7
 ==========================
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-CHANGES in VERSION 2.7.5
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+CHANGES in VERSION 2.7.6
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 * `Legend()`: add a new argument `grob`.
10 12
 
Browse code

remove zoom argument from anno_empty()

Zuguang Gu authored on 26/01/2021 16:10:51
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1 1
 CHANGES in VERSION 2.7.5
2 2
 
3
+* discrete numeric legend labels are in correct order now.
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+
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+==========================
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+
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+CHANGES in VERSION 2.7.5
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+
3 9
 * `Legend()`: add a new argument `grob`.
4 10
 
5 11
 ==========================
Browse code

support to directly use grob in Legend()

Zuguang Gu authored on 24/01/2021 08:39:14
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@@ -1,5 +1,11 @@
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 CHANGES in VERSION 2.7.5
2 2
 
3
+* `Legend()`: add a new argument `grob`.
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+
5
+==========================
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+
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+CHANGES in VERSION 2.7.5
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+
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 * `anno_block()`: add `labels_offset` and `labels_just`.
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 * `anno_lines()`: `show_points` can be a vector.
5 11
 * `pheatmap()`: support `kmeans_k`.
Browse code

support kmeans_k in pheatmap()

Zuguang Gu authored on 22/01/2021 10:25:28
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@@ -1,7 +1,8 @@
1 1
 CHANGES in VERSION 2.7.5
2 2
 
3
-* `anno_block`: add `labels_offset` and `labels_just`.
4
-* `anno_lines`: `show_points` can be a vector.
3
+* `anno_block()`: add `labels_offset` and `labels_just`.
4
+* `anno_lines()`: `show_points` can be a vector.
5
+* `pheatmap()`: support `kmeans_k`.
5 6
 
6 7
 ==========================
7 8
 
Browse code

anno_block(): add labels_offset and labels_just argument

Zuguang Gu authored on 22/01/2021 09:39:05
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@@ -1,3 +1,10 @@
1
+CHANGES in VERSION 2.7.5
2
+
3
+* `anno_block`: add `labels_offset` and `labels_just`.
4
+* `anno_lines`: `show_points` can be a vector.
5
+
6
+==========================
7
+
1 8
 CHANGES in VERSION 2.7.4
2 9
 
3 10
 * add `save_last` option in `ht_opt()`.
Browse code

add save_last option

Zuguang Gu authored on 31/12/2020 09:02:28
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@@ -1,3 +1,9 @@
1
+CHANGES in VERSION 2.7.4
2
+
3
+* add `save_last` option in `ht_opt()`.
4
+
5
+==========================
6
+
1 7
 CHANGES in VERSION 2.7.1
2 8
 
3 9
 * `normalize_comb_mat()`: add `full_comb_sets` and `complement_set` arguments to control
Browse code

move code for interactive heatmap to InteractiveComplexHeatmap package

Zuguang Gu authored on 14/12/2020 08:38:56
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@@ -13,6 +13,7 @@ CHANGES in VERSION 2.7.1
13 13
 * print messages if directly sending `anno_*()` functions to `top_annotation` or similar arguments.
14 14
 * `pheatmap()`: set heatmap name to " " so that there is no legend title by default.
15 15
 * also translate `stats::heatmap()` and `gplots::heatmap.2()`.
16
+* move all code for interactive heatmap to InteractiveComplexHeatmap package.
16 17
 
17 18
 ========================
18 19
 
Browse code

translate stats::heatmap() and gplots::heatmap.2()

Zuguang Gu authored on 13/12/2020 20:54:51
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@@ -12,6 +12,7 @@ CHANGES in VERSION 2.7.1
12 12
 * add `bin_genome()` and `normalize_genomic_signals_to_bins()`
13 13
 * print messages if directly sending `anno_*()` functions to `top_annotation` or similar arguments.
14 14
 * `pheatmap()`: set heatmap name to " " so that there is no legend title by default.
15
+* also translate `stats::heatmap()` and `gplots::heatmap.2()`.
15 16
 
16 17
 ========================
17 18
 
Browse code

pheatmap(): change heatmap name to ' ' to turn off legend title by default

Zuguang Gu authored on 01/12/2020 16:03:08
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@@ -11,6 +11,7 @@ CHANGES in VERSION 2.7.1
11 11
 * temporary solution for woking under retina display with Rstudio
12 12
 * add `bin_genome()` and `normalize_genomic_signals_to_bins()`
13 13
 * print messages if directly sending `anno_*()` functions to `top_annotation` or similar arguments.
14
+* `pheatmap()`: set heatmap name to " " so that there is no legend title by default.
14 15
 
15 16
 ========================
16 17
 
Browse code

print message if directly setting anno_*() for 'top_annotation' argument

Zuguang Gu authored on 24/11/2020 08:23:47
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@@ -10,6 +10,7 @@ CHANGES in VERSION 2.7.1
10 10
 * `make_comb_mat()`: print warning messages when there are NA values in the matrix.
11 11
 * temporary solution for woking under retina display with Rstudio
12 12
 * add `bin_genome()` and `normalize_genomic_signals_to_bins()`
13
+* print messages if directly sending `anno_*()` functions to `top_annotation` or similar arguments.
13 14
 
14 15
 ========================
15 16
 
Browse code

add functions to deal with genome-scale heatmaps

Zuguang Gu authored on 22/11/2020 20:40:20
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@@ -9,6 +9,7 @@ CHANGES in VERSION 2.7.1
9 9
 * Fixed a bug that it crashes Rstudio
10 10
 * `make_comb_mat()`: print warning messages when there are NA values in the matrix.
11 11
 * temporary solution for woking under retina display with Rstudio
12
+* add `bin_genome()` and `normalize_genomic_signals_to_bins()`
12 13
 
13 14
 ========================
14 15
 
Browse code

temporary solution for retina display with Rstudio

Zuguang Gu authored on 10/11/2020 10:56:48
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@@ -8,6 +8,7 @@ CHANGES in VERSION 2.7.1
8 8
 * `Legend()`: add `interval_dist` to control the distance of two neighbouring breaks.
9 9
 * Fixed a bug that it crashes Rstudio
10 10
 * `make_comb_mat()`: print warning messages when there are NA values in the matrix.
11
+* temporary solution for woking under retina display with Rstudio
11 12
 
12 13
 ========================
13 14
 
Browse code

make_comb_mat(): print warning messages when NA in the matrix

Zuguang Gu authored on 10/11/2020 07:28:08
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@@ -7,6 +7,7 @@ CHANGES in VERSION 2.7.1
7 7
 * Legends are automatically adjusted according to the device size when resizing the device.
8 8
 * `Legend()`: add `interval_dist` to control the distance of two neighbouring breaks.
9 9
 * Fixed a bug that it crashes Rstudio
10
+* `make_comb_mat()`: print warning messages when there are NA values in the matrix.
10 11
 
11 12
 ========================
12 13
 
Browse code

update news

Zuguang Gu authored on 09/11/2020 22:29:27
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@@ -6,6 +6,7 @@ CHANGES in VERSION 2.7.1
6 6
 * `Legend()`: for title_position == "lefttop", the title position is adjusted.
7 7
 * Legends are automatically adjusted according to the device size when resizing the device.
8 8
 * `Legend()`: add `interval_dist` to control the distance of two neighbouring breaks.
9
+* Fixed a bug that it crashes Rstudio
9 10
 
10 11
 ========================
11 12
 
Browse code

'Legend()': add 'interval_dist' to control the distance of two neighbouring breaks

Zuguang Gu authored on 02/11/2020 08:55:29
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@@ -5,6 +5,7 @@ CHANGES in VERSION 2.7.1
5 5
 * adjust the space of column title according to ggplot2.
6 6
 * `Legend()`: for title_position == "lefttop", the title position is adjusted.
7 7
 * Legends are automatically adjusted according to the device size when resizing the device.
8
+* `Legend()`: add `interval_dist` to control the distance of two neighbouring breaks.
8 9
 
9 10
 ========================
10 11
 
Browse code

revised the messages

Zuguang Gu authored on 01/11/2020 08:44:36
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@@ -4,6 +4,7 @@ CHANGES in VERSION 2.7.1
4 4
   full sets of combination sets.
5 5
 * adjust the space of column title according to ggplot2.
6 6
 * `Legend()`: for title_position == "lefttop", the title position is adjusted.
7
+* Legends are automatically adjusted according to the device size when resizing the device.
7 8
 
8 9
 ========================
9 10
 
Browse code

lefttop legend title has been adjusted

Zuguang Gu authored on 30/10/2020 19:29:11
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@@ -3,6 +3,7 @@ CHANGES in VERSION 2.7.1
3 3
 * `normalize_comb_mat()`: add `full_comb_sets` and `complement_set` arguments to control
4 4
   full sets of combination sets.
5 5
 * adjust the space of column title according to ggplot2.
6
+* `Legend()`: for title_position == "lefttop", the title position is adjusted.
6 7
 
7 8
 ========================
8 9
 
Browse code

finally adjust the space of column title according to ggplot2

Zuguang Gu authored on 30/10/2020 15:10:21
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@@ -1,3 +1,11 @@
1
+CHANGES in VERSION 2.7.1
2
+
3
+* `normalize_comb_mat()`: add `full_comb_sets` and `complement_set` arguments to control
4
+  full sets of combination sets.
5
+* adjust the space of column title according to ggplot2.
6
+
7
+========================
8
+
1 9
 CHANGES in VERSION 2.5.6
2 10
 
3 11
 * `ht_shiny()`: add argument `app`.
Browse code

various improvements

Zuguang Gu authored on 23/10/2020 16:02:23
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@@ -8,7 +8,10 @@ CHANGES in VERSION 2.5.6
8 8
   can set `at` that are not all in the matrix but are in the `col`.
9 9
 * padding of the whole plot and spaces of column titles are adjusted to fit ggplot2 
10 10
 * add `row_gap` and `column_gap` in `Legend()`.
11
-* `oncoPrint()`: now draw legends as `alter_fun`.
11
+* `oncoPrint()`: now draw legends the same as `alter_fun`.
12
+* add a new function `attach_annotation()`.
13
+* legends for row annotations can be grouped with column annotation legends.
14
+* annotation name allows rotations.
12 15
 
13 16
 ======================
14 17
 
Browse code

oncoPrint() draws legends the same as alter_fun

Zuguang Gu authored on 23/10/2020 07:29:40
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@@ -8,6 +8,7 @@ CHANGES in VERSION 2.5.6
8 8
   can set `at` that are not all in the matrix but are in the `col`.
9 9
 * padding of the whole plot and spaces of column titles are adjusted to fit ggplot2 
10 10
 * add `row_gap` and `column_gap` in `Legend()`.
11
+* `oncoPrint()`: now draw legends as `alter_fun`.
11 12
 
12 13
 ======================
13 14
 
Browse code

Legend(): add row_gap and column_gap arguments

Zuguang Gu authored on 22/10/2020 10:44:27
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@@ -7,6 +7,7 @@ CHANGES in VERSION 2.5.6
7 7
   the full color set is still saved, which means, in `heatmap_legend_param` you 
8 8
   can set `at` that are not all in the matrix but are in the `col`.
9 9
 * padding of the whole plot and spaces of column titles are adjusted to fit ggplot2 
10
+* add `row_gap` and `column_gap` in `Legend()`.
10 11
 
11 12
 ======================
12 13
 
Browse code

adjust spacings according to ggplot2

Zuguang Gu authored on 21/10/2020 07:52:11
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@@ -5,7 +5,8 @@ CHANGES in VERSION 2.5.6
5 5
 * change default raster device to `CairoPNG`.
6 6
 * `Heatmap()`: If the discrete `col` covers more than the levels in the matrix,
7 7
   the full color set is still saved, which means, in `heatmap_legend_param` you 
8
-  can set `at` that are not all in the matrix but are in the `col`. 
8
+  can set `at` that are not all in the matrix but are in the `col`.
9
+* padding of the whole plot and spaces of column titles are adjusted to fit ggplot2 
9 10
 
10 11
 ======================
11 12
 
Browse code

col argument can be a super set of the elements in the character matrix

Zuguang Gu authored on 20/10/2020 19:30:27
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@@ -3,6 +3,9 @@ CHANGES in VERSION 2.5.6
3 3
 * `ht_shiny()`: add argument `app`.
4 4
 * `grid.dendrogram()`: change the recursive implementation with iterations.
5 5
 * change default raster device to `CairoPNG`.
6
+* `Heatmap()`: If the discrete `col` covers more than the levels in the matrix,
7
+  the full color set is still saved, which means, in `heatmap_legend_param` you 
8
+  can set `at` that are not all in the matrix but are in the `col`. 
6 9
 
7 10
 ======================
8 11
 
Browse code

change default raster device to CairoPNG

Zuguang Gu authored on 20/10/2020 13:15:35
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@@ -2,6 +2,7 @@ CHANGES in VERSION 2.5.6
2 2
 
3 3
 * `ht_shiny()`: add argument `app`.
4 4
 * `grid.dendrogram()`: change the recursive implementation with iterations.
5
+* change default raster device to `CairoPNG`.
5 6
 
6 7
 ======================
7 8
 
Browse code

fixed the bug of node stack overflow

Zuguang Gu authored on 20/10/2020 07:36:13
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@@ -1,6 +1,7 @@
1 1
 CHANGES in VERSION 2.5.6
2 2
 
3 3
 * `ht_shiny()`: add argument `app`.
4
+* `grid.dendrogram()`: change the recursive implementation with iterations.
4 5
 
5 6
 ======================
6 7
 
Browse code

add argument 'app' to ht_shiny()

Zuguang Gu authored on 14/10/2020 13:05:19
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@@ -1,3 +1,9 @@
1
+CHANGES in VERSION 2.5.6
2
+
3
+* `ht_shiny()`: add argument `app`.
4
+
5
+======================
6
+
1 7
 CHANGES in VERSION 2.5.5
2 8
 
3 9
 * still draw the legend when all values are NA in an annotation.
Browse code

pheatmap(): color mapping is symmetric to zero when scale is set

simplifyEnrichment authored on 13/10/2020 12:40:30
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@@ -8,6 +8,7 @@ CHANGES in VERSION 2.5.5
8 8
 * `HeatmapAnnotation()`: remove colors that are not in the annotations. 
9 9
 * `pheatmap()`: fixed a bug when length(breaks) = length(color) + 1
10 10
 * `pheatmap()`: legend breaks are centered to zero if the matrix is scaled.
11
+* `pheatmap()`: color mapping is symmetric to zero when scale is set.
11 12
 * support ragg package to write temporary png files
12 13
 * `densityHeatmap()`: column dendrogram is reordered by column means for ks method.
13 14
 
Browse code

remove dependency of ragg

Zuguang Gu authored on 11/10/2020 18:24:04
Showing1 changed files
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@@ -9,6 +9,7 @@ CHANGES in VERSION 2.5.5
9 9
 * `pheatmap()`: fixed a bug when length(breaks) = length(color) + 1
10 10
 * `pheatmap()`: legend breaks are centered to zero if the matrix is scaled.
11 11
 * support ragg package to write temporary png files
12
+* `densityHeatmap()`: column dendrogram is reordered by column means for ks method.
12 13
 
13 14
 ======================
14 15
 
Browse code

support agg_png for writing temporary png files

Zuguang Gu authored on 09/10/2020 13:12:56
Showing1 changed files
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@@ -8,6 +8,7 @@ CHANGES in VERSION 2.5.5
8 8
 * `HeatmapAnnotation()`: remove colors that are not in the annotations. 
9 9
 * `pheatmap()`: fixed a bug when length(breaks) = length(color) + 1
10 10
 * `pheatmap()`: legend breaks are centered to zero if the matrix is scaled.
11
+* support ragg package to write temporary png files
11 12
 
12 13
 ======================
13 14
 
Browse code

pheatmap(): legend breaks are centered to zero if the matrix is scaled

Zuguang Gu authored on 09/10/2020 07:50:19
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@@ -7,6 +7,7 @@ CHANGES in VERSION 2.5.5
7 7
 * `ht_opt$TITLE_PADDING` can be set with a unit of length two.
8 8
 * `HeatmapAnnotation()`: remove colors that are not in the annotations. 
9 9
 * `pheatmap()`: fixed a bug when length(breaks) = length(color) + 1
10
+* `pheatmap()`: legend breaks are centered to zero if the matrix is scaled.
10 11
 
11 12
 ======================
12 13
 
Browse code

fixed a bug of pheatmap() when length(breaks) = length(colors) + 1

Zuguang Gu authored on 08/10/2020 19:11:38
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@@ -6,6 +6,7 @@ CHANGES in VERSION 2.5.5
6 6
 * `pheatmap()`: improve the setting of `color` and `breaks`.
7 7
 * `ht_opt$TITLE_PADDING` can be set with a unit of length two.
8 8
 * `HeatmapAnnotation()`: remove colors that are not in the annotations. 
9
+* `pheatmap()`: fixed a bug when length(breaks) = length(color) + 1
9 10
 
10 11
 ======================
11 12
 
Browse code

remove unused colors in annotations

Zuguang Gu authored on 08/10/2020 08:44:52
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@@ -4,6 +4,8 @@ CHANGES in VERSION 2.5.5
4 4
 * add `show_fraction` argument in `anno_oncoprint_barplot()` function to show the fractions
5 5
   of mutations instead of the counts.
6 6
 * `pheatmap()`: improve the setting of `color` and `breaks`.
7
+* `ht_opt$TITLE_PADDING` can be set with a unit of length two.
8
+* `HeatmapAnnotation()`: remove colors that are not in the annotations. 
7 9
 
8 10
 ======================
9 11
 
Browse code

pheatmap(): adjust the setting of color and breaks

simplifyEnrichment authored on 06/10/2020 12:07:17
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@@ -3,6 +3,7 @@ CHANGES in VERSION 2.5.5
3 3
 * still draw the legend when all values are NA in an annotation.
4 4
 * add `show_fraction` argument in `anno_oncoprint_barplot()` function to show the fractions
5 5
   of mutations instead of the counts.
6
+* `pheatmap()`: improve the setting of `color` and `breaks`.
6 7
 
7 8
 ======================
8 9
 
Browse code

add show_fraction argument to show the fraction of mutations

simplifyEnrichment authored on 06/10/2020 08:38:50
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@@ -1,6 +1,8 @@
1 1
 CHANGES in VERSION 2.5.5
2 2
 
3 3
 * still draw the legend when all values are NA in an annotation.
4
+* add `show_fraction` argument in `anno_oncoprint_barplot()` function to show the fractions
5
+  of mutations instead of the counts.
4 6
 
5 7
 ======================
6 8
 
Browse code

still draw the legend when all values are NA in an annotation

Zuguang Gu authored on 30/09/2020 07:23:38
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@@ -1,3 +1,9 @@
1
+CHANGES in VERSION 2.5.5
2
+
3
+* still draw the legend when all values are NA in an annotation.
4
+
5
+======================
6
+
1 7
 CHANGES in VERSION 2.5.4
2 8
 
3 9
 * fixed a bug where slice clusters were wrongly reordered.
Browse code

check matrix dimensions and nobs of annotations when adding them

Zuguang Gu authored on 12/09/2020 12:12:16
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@@ -10,6 +10,8 @@ CHANGES in VERSION 2.5.4
10 10
 * `Legends()`: fixed a bug of mixtype "legend" to "Legend".
11 11
 * now assign correct envir to `decorate_dend()`.
12 12
 * `pheatmap()`: check `NA` in the matrix.
13
+* `grid.dendrogram()`: consider branches with height zero.
14
+* checking the dimension of the matrix and the nobs of annotations when adding them.
13 15
 
14 16
 ========================
15 17
 
Browse code

check NA in pheatmap()

Zuguang Gu authored on 09/09/2020 06:54:18
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@@ -8,6 +8,8 @@ CHANGES in VERSION 2.5.4
8 8
 * support setting graphics on dendrogram nodes.
9 9
 * Add a new vignette "interactive heatmap"
10 10
 * `Legends()`: fixed a bug of mixtype "legend" to "Legend".
11
+* now assign correct envir to `decorate_dend()`.
12
+* `pheatmap()`: check `NA` in the matrix.
11 13
 
12 14
 ========================
13 15
 
Browse code

Legends(): fixed a bug of mistype legend to Legend

Zuguang Gu authored on 18/07/2020 08:35:54
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@@ -7,6 +7,7 @@ CHANGES in VERSION 2.5.4
7 7
 * support better rasterization.
8 8
 * support setting graphics on dendrogram nodes.
9 9
 * Add a new vignette "interactive heatmap"
10
+* `Legends()`: fixed a bug of mixtype "legend" to "Legend".
10 11
 
11 12
 ========================
12 13
 
Browse code

bug fixed

Zuguang Gu authored on 10/07/2020 09:02:24
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@@ -6,6 +6,7 @@ CHANGES in VERSION 2.5.4
6 6
 * `anno_block()`: allows to set height and width.
7 7
 * support better rasterization.
8 8
 * support setting graphics on dendrogram nodes.
9
+* Add a new vignette "interactive heatmap"
9 10
 
10 11
 ========================
11 12
 
Browse code

won't support graphics on dendrogram nodes

Zuguang Gu authored on 05/07/2020 20:11:01
Showing1 changed files
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@@ -5,6 +5,7 @@ CHANGES in VERSION 2.5.4
5 5
 * Legends are nicely placed.
6 6
 * `anno_block()`: allows to set height and width.
7 7
 * support better rasterization.
8
+* support setting graphics on dendrogram nodes.
8 9
 
9 10
 ========================
10 11
 
Browse code

improve rasterization

Zuguang Gu authored on 02/07/2020 10:40:04
Showing1 changed files
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@@ -4,6 +4,7 @@ CHANGES in VERSION 2.5.4
4 4
 * `Heatmap()`: add `border_gp` argument.
5 5
 * Legends are nicely placed.
6 6
 * `anno_block()`: allows to set height and width.
7
+* support better rasterization.
7 8
 
8 9
 ========================
9 10
 
Browse code

anno_block(): allows to set width and height

Zuguang Gu authored on 29/06/2020 15:54:31
Showing1 changed files
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@@ -3,6 +3,7 @@ CHANGES in VERSION 2.5.4
3 3
 * fixed a bug where slice clusters were wrongly reordered.
4 4
 * `Heatmap()`: add `border_gp` argument.
5 5
 * Legends are nicely placed.
6
+* `anno_block()`: allows to set height and width.
6 7
 
7 8
 ========================
8 9
 
Browse code

try to nicely place legends

Zuguang Gu authored on 28/06/2020 20:28:06
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@@ -2,6 +2,7 @@ CHANGES in VERSION 2.5.4
2 2
 
3 3
 * fixed a bug where slice clusters were wrongly reordered.
4 4
 * `Heatmap()`: add `border_gp` argument.
5
+* Legends are nicely placed.
5 6
 
6 7
 ========================
7 8
 
Browse code

bug fixed

Zuguang Gu authored on 28/06/2020 13:14:25
Showing1 changed files
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@@ -1,3 +1,10 @@
1
+CHANGES in VERSION 2.5.4
2
+
3
+* fixed a bug where slice clusters were wrongly reordered.
4
+* `Heatmap()`: add `border_gp` argument.
5
+
6
+========================
7
+
1 8
 CHANGES in VERSION 2.5.3
2 9
 
3 10
 * add `selectArea()`/`selectPosition()` which allows interactively select a region from 
Browse code

anno_mark(), anno_zoom(); print message under RStudio

Zuguang Gu authored on 14/06/2020 20:36:59
Showing1 changed files
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@@ -9,6 +9,9 @@ CHANGES in VERSION 2.5.3
9 9
 * `anno_image()`: fixed a bug that images are not reordered.
10 10
 * `anno_mark()`: now expression is correctly supported.
11 11
 * `anno_zoom()`: order of index in `panel_fun` is adjusted to the order in the heatmap
12
+* `list_to_matrix()`: convert elements to characters.
13
+* print messages for `anno_mark()`, `anno_zoom()`, `draw_legend()` (if legends are wrapped) 
14
+  if working under RStudio.
12 15
 
13 16
 ========================
14 17
 
Browse code

order in 'align_to' is adjusted

Zuguang Gu authored on 08/06/2020 13:26:45
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@@ -8,6 +8,7 @@ CHANGES in VERSION 2.5.3
8 8
 * `discrete_legend_body()`: adjust ncol and nrow if there are empty rows and columns in the layout.
9 9
 * `anno_image()`: fixed a bug that images are not reordered.
10 10
 * `anno_mark()`: now expression is correctly supported.
11
+* `anno_zoom()`: order of index in `panel_fun` is adjusted to the order in the heatmap
11 12
 
12 13
 ========================
13 14
 
Browse code

anno_mark(): expression is correctly supported

Zuguang Gu authored on 02/06/2020 09:59:27
Showing1 changed files
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@@ -7,6 +7,7 @@ CHANGES in VERSION 2.5.3
7 7
 * `default_col()`: print a message if there are outliers in the matrix.
8 8
 * `discrete_legend_body()`: adjust ncol and nrow if there are empty rows and columns in the layout.
9 9
 * `anno_image()`: fixed a bug that images are not reordered.
10
+* `anno_mark()`: now expression is correctly supported.
10 11
 
11 12
 ========================
12 13
 
Browse code

anno_image(): fixed a bug that images are not reordered

Zuguang Gu authored on 21/05/2020 21:13:54
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@@ -6,6 +6,7 @@ CHANGES in VERSION 2.5.3
6 6
 * `col` in `Heatmap()` accpets a `ColorMapping` object.
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 * `default_col()`: print a message if there are outliers in the matrix.
8 8
 * `discrete_legend_body()`: adjust ncol and nrow if there are empty rows and columns in the layout.
9
+* `anno_image()`: fixed a bug that images are not reordered.
9 10
 
10 11
 ========================
11 12
 
Browse code

discrete_legend_body(): adjust ncol and nrow if there are empty rows and columns in the layout.

Zuguang Gu authored on 19/05/2020 09:31:32
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@@ -5,6 +5,7 @@ CHANGES in VERSION 2.5.3
5 5
 * export the heatmap as a shiny app!!!
6 6
 * `col` in `Heatmap()` accpets a `ColorMapping` object.
7 7
 * `default_col()`: print a message if there are outliers in the matrix.
8
+* `discrete_legend_body()`: adjust ncol and nrow if there are empty rows and columns in the layout.
8 9
 
9 10
 ========================
10 11
 
Browse code

default_col():print messages if there are outliers

Zuguang Gu authored on 18/05/2020 20:10:51
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@@ -4,6 +4,7 @@ CHANGES in VERSION 2.5.3
4 4
   the heatmaps.
5 5
 * export the heatmap as a shiny app!!!
6 6
 * `col` in `Heatmap()` accpets a `ColorMapping` object.
7
+* `default_col()`: print a message if there are outliers in the matrix.
7 8
 
8 9
 ========================
9 10
 
Browse code

export heatmaps as a shiny app

Zuguang Gu authored on 17/05/2020 13:20:00
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1 1
 CHANGES in VERSION 2.5.3
2 2
 
3
-* add `selectArea()` which allows interactively select a region from 
3
+* add `selectArea()`/`selectPosition()` which allows interactively select a region from 
4 4
   the heatmaps.
5
+* export the heatmap as a shiny app!!!
6
+* `col` in `Heatmap()` accpets a `ColorMapping` object.
5 7
 
6 8
 ========================
7 9
 
Browse code

add selectArea()

Zuguang Gu authored on 14/05/2020 06:36:17
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@@ -1,3 +1,10 @@
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+CHANGES in VERSION 2.5.3
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+
3
+* add `selectArea()` which allows interactively select a region from 
4
+  the heatmaps.
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+
6
+========================
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+
1 8
 CHANGES in VERSION 2.5.2
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3 10
 * translate pheatmap to Heatmap
Browse code

UpSet(): change the annotation name

Zuguang Gu authored on 13/05/2020 08:29:39
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 CHANGES in VERSION 2.5.2
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3 3
 * translate pheatmap to Heatmap
4
+* `upset_top_annotation()` and `upset_right_annotation()`: the names of the annotations
5
+   are changed to `intersection_size`, `set_size` and `union_size`.
6
+* `list_components()`: adds `pattern` argument.
4 7
 
5 8
 ========================
6 9
 
Browse code

increase version number

Zuguang Gu authored on 06/05/2020 09:54:55
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1
+CHANGES in VERSION 2.5.2
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+
3
+* translate pheatmap to Heatmap
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+
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+========================
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+
1 7
 CHANGES in VERSION 2.5.1
2 8
 
3 9
 * A temporary solution of the sum of two complicated units (in temp.R).
4
-* translate pheatmap to Heatmap
5 10
 
6 11
 ========================
7 12
 
Browse code

translate pheatmap to Heatmap

Zuguang Gu authored on 06/05/2020 07:21:34
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1 1
 CHANGES in VERSION 2.5.1
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3 3
 * A temporary solution of the sum of two complicated units (in temp.R).
4
+* translate pheatmap to Heatmap
4 5
 
5 6
 ========================
6 7
 
Browse code

add temporary sum.unit()

Zuguang Gu authored on 29/04/2020 10:15:07
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1
+CHANGES in VERSION 2.5.1
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+
3
+* A temporary solution of the sum of two complicated units (in temp.R).
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+
5
+========================
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+
1 7
 CHANGES in VERSION 2.3.4
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3 9
 * add `alter_graphic()` to automatically generate alteration graphic functions.
Browse code

updat docs

Zuguang Gu authored on 13/04/2020 12:17:38
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3 3
 * add `alter_graphic()` to automatically generate alteration graphic functions.
4 4
 * add `label`/`annotation_label` argument in `SingleAnnotation()` and `HeatmapAnnotation()`.
5 5
 * improved the subsetting methods for `comb_mat` class
6
+* rewrite `smartAlign2()`
6 7
 
7 8
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8 9
 
Browse code

improved subset method for comb_mat class

Zuguang Gu authored on 06/04/2020 13:08:25
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1 1
 CHANGES in VERSION 2.3.4
2 2
 
3 3
 * add `alter_graphic()` to automatically generate alteration graphic functions.
4
+* add `label`/`annotation_label` argument in `SingleAnnotation()` and `HeatmapAnnotation()`.
5
+* improved the subsetting methods for `comb_mat` class
4 6
 
5 7
 ========================
6 8
 
Browse code

add 'alter_graphic()' function to automatically generate alteration graphic functions

Zuguang Gu authored on 03/04/2020 19:56:52
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+CHANGES in VERSION 2.3.4
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+
3
+* add `alter_graphic()` to automatically generate alteration graphic functions.
4
+
5
+========================
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+
1 7
 CHANGES in VERSION 2.3.3
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3 9
 * support **gridtext** package
Browse code

add 'show_name' argument in 'anno_block()' function

Zuguang Gu authored on 01/04/2020 12:49:26
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@@ -8,6 +8,7 @@ CHANGES in VERSION 2.3.3
8 8
   is turned on and the message should be printed to users.
9 9
 * UpSet plots: optimize the processing of many sets (current solution consumes huge memory)
10 10
 * UpSet plots: the "intersect" and "union" modes are currectly calculated.
11
+* `anno_block()`: add `show_name` argument.
11 12
 
12 13
 ========================
13 14
 
Browse code

improved upset plots

Zuguang Gu authored on 26/03/2020 20:10:50
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2 2
 
3 3
 * support **gridtext** package
4 4
 * fixed the bug of node stack overflow when there are many identical rows for drawing the dendrogram.
5
+  see (http://www.thinkingincrowd.me/2016/06/06/How-to-avoid-Stack-overflow-error-on-recursive/)
5 6
 * support to set legend gaps
6 7
 * print important messages, e.g. when number of rows are more than 2000, interanlly use_raster 
7 8
   is turned on and the message should be printed to users.
9
+* UpSet plots: optimize the processing of many sets (current solution consumes huge memory)
10
+* UpSet plots: the "intersect" and "union" modes are currectly calculated.
8 11
 
9 12
 ========================
10 13
 
Browse code

print important messages

Zuguang Gu authored on 22/03/2020 11:27:49
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3 3
 * support **gridtext** package
4 4
 * fixed the bug of node stack overflow when there are many identical rows for drawing the dendrogram.
5 5
 * support to set legend gaps
6
+* print important messages, e.g. when number of rows are more than 2000, interanlly use_raster 
7
+  is turned on and the message should be printed to users.
6 8
 
7 9
 ========================
8 10
 
Browse code

print important messages

Zuguang Gu authored on 22/03/2020 11:26:41
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1 1
 CHANGES in VERSION 2.3.3
2 2
 
3 3
 * support **gridtext** package
4
-* fixed the bug of node stack overflow when there are many identical rows for drawing the dendrogram
4
+* fixed the bug of node stack overflow when there are many identical rows for drawing the dendrogram.
5
+* support to set legend gaps
5 6
 
6 7
 ========================
7 8
 
Browse code

support setting legend gaps

Zuguang Gu authored on 22/03/2020 11:15:01
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1 1
 CHANGES in VERSION 2.3.3
2 2
 
3 3
 * support **gridtext** package
4
+* fixed the bug of node stack overflow when there are many identical rows for drawing the dendrogram
4 5
 
5 6
 ========================
6 7
 
Browse code

support gridtext

Zuguang Gu authored on 21/03/2020 14:32:08
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+CHANGES in VERSION 2.3.3
2
+
3
+* support **gridtext** package
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+
5
+========================
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+
1 7
 CHANGES in VERSION 2.3.2
2 8
 
3 9
 * `anno_simple()`: fixed a bug when pch are all NA in a slice
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5 11
 * move scripts in test_not_run/ to tests/ folder
6 12
 * `Heatmap()`: `cluster_row_slice`/`cluster_column_slice` set to TRUE
7 13
   by default for character matrix and when dendrogram is already provided.
8
-* `smartAlign2()`: improved the code
14
+* `smartAlign2()`: improved the code that positions are correctly calculated.
15
+* row titles are in the correct order if they are set as "template".
9 16
 
10 17
 ========================
11 18
 
Browse code

smartAlign2(): correctly calculate positions of boxes

Zuguang Gu authored on 20/03/2020 19:42:24
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5 5
 * move scripts in test_not_run/ to tests/ folder
6 6
 * `Heatmap()`: `cluster_row_slice`/`cluster_column_slice` set to TRUE
7 7
   by default for character matrix and when dendrogram is already provided.
8
+* `smartAlign2()`: improved the code
8 9
 
9 10
 ========================
10 11
 
Browse code

set cluster_row_slice and cluster_column_slice for character matrix

Zuguang Gu authored on 19/03/2020 21:00:22
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3 3
 * `anno_simple()`: fixed a bug when pch are all NA in a slice
4 4
 * adjust code according to grid 4.0.
5 5
 * move scripts in test_not_run/ to tests/ folder
6
+* `Heatmap()`: `cluster_row_slice`/`cluster_column_slice` set to TRUE
7
+  by default for character matrix and when dendrogram is already provided.
6 8
 
7 9
 ========================
8 10
 
Browse code

use unitType(, recurse=T) to test absolute units

Zuguang Gu authored on 05/03/2020 21:39:57
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 CHANGES in VERSION 2.3.2
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3 3
 * `anno_simple()`: fixed a bug when pch are all NA in a slice
4
+* adjust code according to grid 4.0.
5
+* move scripts in test_not_run/ to tests/ folder
4 6
 
5 7
 ========================
6 8
 
Browse code

adjust code according to grid 4.0.0

Zuguang Gu authored on 02/03/2020 21:10:16
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 CHANGES in VERSION 2.3.2
2 2
 
3
-* support gridtext
4 3
 * `anno_simple()`: fixed a bug when pch are all NA in a slice
5 4
 
6 5
 ========================
Browse code

anno_simple(): fixed a bug when all pch are NA in a slice

Zuguang Gu authored on 25/02/2020 14:51:37
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1 1
 CHANGES in VERSION 2.3.2
2 2
 
3 3
 * support gridtext
4
+* `anno_simple()`: fixed a bug when pch are all NA in a slice
4 5
 
5 6
 ========================
6 7
 
Browse code

support gridtext

Zuguang Gu authored on 05/02/2020 07:34:10
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+CHANGES in VERSION 2.3.2
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+
3
+* support gridtext
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+
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+========================
6
+
1 7
 CHANGES in VERSION 2.3.1
2 8
 
3 9
 * `anno_points()`: allows images as symbols.
Browse code

oncoPrint(): print messages if NA in the matrix

jokergoo authored on 13/01/2020 10:58:23
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3 3
 * `anno_points()`: allows images as symbols.
4 4
 * add `HEATMAP_LEGEND_PADDING` and `ANNOTATION_LEGEND_PADDING` options in `ht_opt`
5
+* `oncoPrint()`: print messages if there are NA values in the input matrix
5 6
 
6 7
 ========================
7 8
 
jokergoo authored on 09/12/2019 11:08:13
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anno_points(): images can be point symbols

jokergoo authored on 09/12/2019 11:06:42
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+CHANGES in VERSION 2.3.1
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+
3
+* `anno_points()`: allows images as symbols.
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+
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+========================
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+
1 7
 CHANGES in VERSION 2.1.1
2 8
 
3 9
 * `Heatmap()`: give error when heatmap has empty string as its name.
Browse code

add HEATMAP_LEGEND_PADDING and ANNOTATION_LEGEND_PADDING options

Zuguang Gu authored on 09/11/2019 09:18:39
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+CHANGES in VERSION 2.3.1
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+
3
+* add `HEATMAP_LEGEND_PADDING` and `ANNOTATION_LEGEND_PADDING` options in `ht_opt`
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+
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+========================
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+
1 7
 CHANGES in VERSION 2.1.1
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3 9
 * `Heatmap()`: give error when heatmap has empty string as its name.
Browse code

adjust the order of legend labels

Zuguang Gu authored on 20/10/2019 09:37:25
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2 2
 
3 3
 * `Heatmap()`: give error when heatmap has empty string as its name.
4 4
 * `anno_mark()`: text positions are correctly calculated now with rotations.
5
+* The order of legend labels are ordered by either `sort` or `levels`.
5 6
 
6 7
 ========================
7 8
 
Browse code

update

Zuguang Gu authored on 20/10/2019 06:57:30
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 CHANGES in VERSION 2.1.1
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3 3
 * `Heatmap()`: give error when heatmap has empty string as its name.
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-* `anno_mark()`: text positions are correctly calcualted now with rotations.
4
+* `anno_mark()`: text positions are correctly calculated now with rotations.
5 5
 
6 6
 ========================
7 7
 
Browse code

update

Zuguang Gu authored on 19/10/2019 18:58:27
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 CHANGES in VERSION 2.1.1
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3 3
 * `Heatmap()`: give error when heatmap has empty string as its name.
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+* `anno_mark()`: text positions are correctly calcualted now with rotations.
4 5
 
5 6
 ========================
6 7
 
Browse code

heatmap name cannot be empty string

Zuguang Gu authored on 12/10/2019 10:01:00
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+CHANGES in VERSION 2.1.1
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+
3
+* `Heatmap()`: give error when heatmap has empty string as its name.
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+
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+========================
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+
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 CHANGES in VERSION 2.1.0
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3 9
 * check the length of the clustering objects and the matrix rows/columns
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12 18
 * `Heatmap()`: add `jitter` argument to add tiny random shift to original matrix. 
13 19
    It is mainly to solve the problem of "Error: node stack overflow"
14 20
    when there are too many identical rows/columns for plotting the dendrograms.
15
-* `Heatmap()`: give error when heatmap has empty string as its name.
16 21
 
17 22
 ========================
18 23
 
Browse code

heatmap name cannot be empty string

Zuguang Gu authored on 12/10/2019 09:51:06
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@@ -12,6 +12,7 @@ CHANGES in VERSION 2.1.0
12 12
 * `Heatmap()`: add `jitter` argument to add tiny random shift to original matrix. 
13 13
    It is mainly to solve the problem of "Error: node stack overflow"
14 14
    when there are too many identical rows/columns for plotting the dendrograms.
15
+* `Heatmap()`: give error when heatmap has empty string as its name.
15 16
 
16 17
 ========================
17 18
 
Browse code

add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
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9 9
 * `densityHeatmap()`: `col` can be set as a function
10 10
 * add `cluster_rows`/`cluster_columns` in `oncoPrint()`
11 11
 * legend labels support symbols
12
+* `Heatmap()`: add `jitter` argument to add tiny random shift to original matrix. 
13
+   It is mainly to solve the problem of "Error: node stack overflow"
14
+   when there are too many identical rows/columns for plotting the dendrograms.
12 15
 
13 16
 ========================
14 17
 
Browse code

densithHeatmap(): col now can be a function

Zuguang Gu authored on 26/09/2019 08:53:12
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Browse code

densithHeatmap(): col now can be a function

Zuguang Gu authored on 26/09/2019 08:52:20
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6 6
 * `draw_legend()`: legends for annotations with the same names are merged
7 7
 * `densityHeatmap()`: `ylim` works as it is expected.
8 8
 * add `cluster_row_slices` and `cluster_column_slices` to `draw,HeatmapList-method()`
9
+* `densityHeatmap()`: `col` can be set as a function
9 10
 
10 11
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11 12
 
Browse code

legends support symbols as labels

Zuguang Gu authored on 25/09/2019 07:48:09
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7 7
 * `densityHeatmap()`: `ylim` works as it is expected.
8 8
 * add `cluster_row_slices` and `cluster_column_slices` to `draw,HeatmapList-method()`
9 9
 * add `cluster_rows`/`cluster_columns` in `oncoPrint()`
10
+* legend labels support symbols
10 11
 
11 12
 ========================
12 13
 
Browse code

support cluster_rows/cluster_columns in oncoPrint()

Zuguang Gu authored on 15/09/2019 10:01:02
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6 6
 * `draw_legend()`: legends for annotations with the same names are merged
7 7
 * `densityHeatmap()`: `ylim` works as it is expected.
8 8
 * add `cluster_row_slices` and `cluster_column_slices` to `draw,HeatmapList-method()`
9
+* add `cluster_rows`/`cluster_columns` in `oncoPrint()`
9 10
 
10 11
 ========================
11 12
 
Zuguang Gu authored on 02/09/2019 20:19:44
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densityHeatmap() supports to self-define ylim

Zuguang Gu authored on 02/09/2019 20:19:02
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4 4
 * `anno_oncoprint_barplot()`: add `ylim` argumnet
5 5
 * `anno_mark()`: add `labels_rot` argument
6 6
 * `draw_legend()`: legends for annotations with the same names are merged
7
+* `densityHeatmap()`: `ylim` works as it is expected.
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8 9
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9 10
 
Browse code

add cluster_row_slices and cluster_column_slices to draw()

Zuguang Gu authored on 02/09/2019 09:19:16
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4 4
 * `anno_oncoprint_barplot()`: add `ylim` argumnet
5 5
 * `anno_mark()`: add `labels_rot` argument
6 6
 * `draw_legend()`: legends for annotations with the same names are merged
7
+* add `cluster_row_slices` and `cluster_column_slices` to `draw,HeatmapList-method()`
7 8
 
8 9
 ========================
9 10
 
Browse code

legends for annotations with the same names are merged

Zuguang Gu authored on 06/08/2019 07:40:38
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3 3
 * check the length of the clustering objects and the matrix rows/columns
4 4
 * `anno_oncoprint_barplot()`: add `ylim` argumnet
5 5
 * `anno_mark()`: add `labels_rot` argument
6
+* `draw_legend()`: legends for annotations with the same names are merged
6 7
 
7 8
 ========================
8 9
 
Browse code

add labels_rot argument to anno_mark()

Zuguang Gu authored on 02/07/2019 20:34:44
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3 3
 * check the length of the clustering objects and the matrix rows/columns
4 4
 * `anno_oncoprint_barplot()`: add `ylim` argumnet
5
+* `anno_mark()`: add `labels_rot` argument
5 6
 
6 7
 ========================
7 8
 
Browse code

update NEWS

Zuguang Gu authored on 10/06/2019 16:23:38
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 CHANGES in VERSION 2.1.0
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 * check the length of the clustering objects and the matrix rows/columns
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+* `anno_oncoprint_barplot()`: add `ylim` argumnet
4 5
 
5 6
 ========================
6 7
 
Browse code

check consistency of clustering objects and matrix

Zuguang Gu authored on 08/06/2019 05:49:40
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+CHANGES in VERSION 2.1.0