Zuguang Gu authored on 08/02/2023 14:00:01
| ... | ... |
@@ -4,6 +4,7 @@ CHANGES in VERSION 2.15.1 |
| 4 | 4 |
* `SingleAnnotation()`: correctly calculate the max width/height of a vector of texts. |
| 5 | 5 |
* `to_unit()`: fixed a bug when the unit is negative. |
| 6 | 6 |
* `Legend()`: add `tick_length` argument. |
| 7 |
+* `Legend()`: colors are correctly calculated when differences between `at` are not equal. |
|
| 7 | 8 |
|
| 8 | 9 |
======================= |
| 9 | 10 |
|
Zuguang Gu authored on 08/02/2023 12:51:48
| ... | ... |
@@ -3,6 +3,7 @@ CHANGES in VERSION 2.15.1 |
| 3 | 3 |
* `Legend()`: allows `NA` in `pch`. |
| 4 | 4 |
* `SingleAnnotation()`: correctly calculate the max width/height of a vector of texts. |
| 5 | 5 |
* `to_unit()`: fixed a bug when the unit is negative. |
| 6 |
+* `Legend()`: add `tick_length` argument. |
|
| 6 | 7 |
|
| 7 | 8 |
======================= |
| 8 | 9 |
|
Zuguang Gu authored on 08/12/2022 14:49:02
Zuguang Gu authored on 24/11/2022 13:51:12
| ... | ... |
@@ -1,3 +1,10 @@ |
| 1 |
+CHANGES in VERSION 2.15.1 |
|
| 2 |
+ |
|
| 3 |
+* `Legend()`: allows `NA` in `pch`. |
|
| 4 |
+* `SingleAnnotation()`: correctly calculate the max width/height of a vector of texts. |
|
| 5 |
+ |
|
| 6 |
+======================= |
|
| 7 |
+ |
|
| 1 | 8 |
CHANGES in VERSION 2.13.4 |
| 2 | 9 |
|
| 3 | 10 |
* `anno_barplot()`: fixed a bug when split is set, the bars are wrongly plotted under besides = TRUE. |
Zuguang Gu authored on 27/10/2022 09:23:08
| ... | ... |
@@ -2,6 +2,7 @@ CHANGES in VERSION 2.13.4 |
| 2 | 2 |
|
| 3 | 3 |
* `anno_barplot()`: fixed a bug when split is set, the bars are wrongly plotted under besides = TRUE. |
| 4 | 4 |
* `anno_boxplot()`: add two new argumetn: `add_points` and `pt_gp`. |
| 5 |
+* fixed a bug of size of column title wrongly calculated. |
|
| 5 | 6 |
|
| 6 | 7 |
======================== |
| 7 | 8 |
|
Zuguang Gu authored on 27/10/2022 08:59:57
Zuguang Gu authored on 27/10/2022 08:33:37
| ... | ... |
@@ -1,3 +1,9 @@ |
| 1 |
+CHANGES in VERSION 2.13.4 |
|
| 2 |
+ |
|
| 3 |
+* `anno_barplot()`: fixed a bug when split is set, the bars are wrongly plotted under besides = TRUE. |
|
| 4 |
+ |
|
| 5 |
+======================== |
|
| 6 |
+ |
|
| 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. |
Zuguang Gu authored on 28/09/2022 13:59:00
| ... | ... |
@@ -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. |
| 5 | 5 |
* `oncoPrint()`: Add `pct_include` argument. |
| 6 |
+* `anno_density()`: fixed a bug where `xlim` is ignored for "heatmap". |
|
| 6 | 7 |
|
| 7 | 8 |
======================== |
| 8 | 9 |
|
Zuguang Gu authored on 02/09/2022 07:57:24
| ... | ... |
@@ -2,6 +2,7 @@ CHANGES in VERSION 2.13.2 |
| 2 | 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. |
| 5 |
+* `oncoPrint()`: Add `pct_include` argument. |
|
| 5 | 6 |
|
| 6 | 7 |
======================== |
| 7 | 8 |
|
Zuguang Gu authored on 01/09/2022 19:33:43
Zuguang Gu authored on 31/08/2022 14:37:52
Zuguang Gu authored on 27/07/2022 09:51:25
Zuguang Gu authored on 31/05/2022 13:27:23
Zuguang Gu authored on 31/05/2022 09:48:27
Zuguang Gu authored on 12/04/2022 16:11:28
| ... | ... |
@@ -1,3 +1,10 @@ |
| 1 |
+CHANGES in VERSION 2.11.2 |
|
| 2 |
+ |
|
| 3 |
+* discrete color mapping: when heatmap_param_list$at is set, it is reduced accordingly |
|
| 4 |
+ to `col`. |
|
| 5 |
+ |
|
| 6 |
+======================= |
|
| 7 |
+ |
|
| 1 | 8 |
CHANGES in VERSION 2.11.1 |
| 2 | 9 |
|
| 3 | 10 |
* add a global option `ht_opt$COLOR` to control colors for continuous color mapping. |
Zuguang Gu authored on 02/04/2022 15:52:11
| ... | ... |
@@ -8,6 +8,8 @@ CHANGES in VERSION 2.11.1 |
| 8 | 8 |
* add `show_name` argument in `anno_empty()`. |
| 9 | 9 |
* the validation of annotations in `HeatmapAnnotation()` is simplified. |
| 10 | 10 |
* add `anno_numeric()`. |
| 11 |
+* when `rect_gp = gpar(type = "none")`, `use_raster` is enforced to be FALSE. |
|
| 12 |
+* "global variables" outside `cell_fun`/`layer_fun` are aotumatially identified and saved locally. |
|
| 11 | 13 |
|
| 12 | 14 |
========================= |
| 13 | 15 |
|
Zuguang Gu authored on 18/02/2022 19:51:49
| ... | ... |
@@ -6,6 +6,8 @@ CHANGES in VERSION 2.11.1 |
| 6 | 6 |
* `anno_block()`: add `align_to` argument. |
| 7 | 7 |
* add `anno_text_box()` and `grid.text_box()`. |
| 8 | 8 |
* add `show_name` argument in `anno_empty()`. |
| 9 |
+* the validation of annotations in `HeatmapAnnotation()` is simplified. |
|
| 10 |
+* add `anno_numeric()`. |
|
| 9 | 11 |
|
| 10 | 12 |
========================= |
| 11 | 13 |
|
Zuguang Gu authored on 03/02/2022 09:53:48
| ... | ... |
@@ -3,6 +3,9 @@ CHANGES in VERSION 2.11.1 |
| 3 | 3 |
* add a global option `ht_opt$COLOR` to control colors for continuous color mapping. |
| 4 | 4 |
* `annotation_label` can be an `expression` object. |
| 5 | 5 |
* `recycle_gp()`: now consider when n = 0. |
| 6 |
+* `anno_block()`: add `align_to` argument. |
|
| 7 |
+* add `anno_text_box()` and `grid.text_box()`. |
|
| 8 |
+* add `show_name` argument in `anno_empty()`. |
|
| 6 | 9 |
|
| 7 | 10 |
========================= |
| 8 | 11 |
|
Zuguang Gu authored on 13/11/2021 10:42:20
Zuguang Gu authored on 08/11/2021 18:36:48
Zuguang Gu authored on 08/11/2021 12:27:29
| ... | ... |
@@ -1,3 +1,9 @@ |
| 1 |
+CHANGES in VERSION 2.11.1 |
|
| 2 |
+ |
|
| 3 |
+* add a global option `ht_opt$COLOR` to control colors for continuous color mapping. |
|
| 4 |
+ |
|
| 5 |
+========================= |
|
| 6 |
+ |
|
| 1 | 7 |
CHANGES in VERSION 2.9.4 |
| 2 | 8 |
|
| 3 | 9 |
* fixed a bug of missing right annotation legends for vertically concatenated heatmaps. |
Zuguang Gu authored on 25/10/2021 10:18:45
| ... | ... |
@@ -5,6 +5,7 @@ CHANGES in VERSION 2.9.4 |
| 5 | 5 |
* 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. |
| 7 | 7 |
* add `plot()` method for `Heatmap` and `HeatmapList` classes. |
| 8 |
+* add `anno_customize()`. |
|
| 8 | 9 |
|
| 9 | 10 |
======================== |
| 10 | 11 |
|
Zuguang Gu authored on 29/09/2021 08:38:35
| ... | ... |
@@ -4,6 +4,7 @@ CHANGES in VERSION 2.9.4 |
| 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 | 6 |
* add a new argument `beside` in `anno_barplot()` to position bars beside each other. |
| 7 |
+* add `plot()` method for `Heatmap` and `HeatmapList` classes. |
|
| 7 | 8 |
|
| 8 | 9 |
======================== |
| 9 | 10 |
|
Zuguang Gu authored on 28/09/2021 11:13:16
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 28/09/2021 09:20:28
| ... | ... |
@@ -1,6 +1,8 @@ |
| 1 | 1 |
CHANGES in VERSION 2.9.4 |
| 2 | 2 |
|
| 3 | 3 |
* fixed a bug of missing right annotation legends for vertically concatenated heatmaps. |
| 4 |
+* `Legend()`: support `border` to be set to `asis`. |
|
| 5 |
+* Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height). |
|
| 4 | 6 |
|
| 5 | 7 |
======================== |
| 6 | 8 |
|
Zuguang Gu authored on 09/09/2021 11:56:42
Zuguang Gu authored on 08/09/2021 13:02:52
Zuguang Gu authored on 08/09/2021 08:28:57
| ... | ... |
@@ -10,6 +10,7 @@ CHANGES in VERSION 2.9.3 |
| 10 | 10 |
* `anno_barplot()`: allows to add numbers on top of bars. |
| 11 | 11 |
* `UpSet()`: axis labels are automatically formated for genomic coordinates. |
| 12 | 12 |
* `AnnotationFunction()`: add a new argument `cell_fun`. |
| 13 |
+* When the dendrogram height is zero, the corresponding viewport has scale (0, 1). |
|
| 13 | 14 |
|
| 14 | 15 |
========================= |
| 15 | 16 |
|
Zuguang Gu authored on 04/08/2021 08:55:06
| ... | ... |
@@ -9,6 +9,7 @@ CHANGES in VERSION 2.9.3 |
| 9 | 9 |
same values. |
| 10 | 10 |
* `anno_barplot()`: allows to add numbers on top of bars. |
| 11 | 11 |
* `UpSet()`: axis labels are automatically formated for genomic coordinates. |
| 12 |
+* `AnnotationFunction()`: add a new argument `cell_fun`. |
|
| 12 | 13 |
|
| 13 | 14 |
========================= |
| 14 | 15 |
|
Zuguang Gu authored on 03/08/2021 21:05:45
| ... | ... |
@@ -8,6 +8,7 @@ CHANGES in VERSION 2.9.3 |
| 8 | 8 |
* discrete annotations: neighbour grids are merged into one single grid if they have the |
| 9 | 9 |
same values. |
| 10 | 10 |
* `anno_barplot()`: allows to add numbers on top of bars. |
| 11 |
+* `UpSet()`: axis labels are automatically formated for genomic coordinates. |
|
| 11 | 12 |
|
| 12 | 13 |
========================= |
| 13 | 14 |
|
Zuguang Gu authored on 03/08/2021 12:22:45
| ... | ... |
@@ -7,6 +7,7 @@ CHANGES in VERSION 2.9.3 |
| 7 | 7 |
* legends: fixed a bug of the grid heights were not correctedly calculated. |
| 8 | 8 |
* discrete annotations: neighbour grids are merged into one single grid if they have the |
| 9 | 9 |
same values. |
| 10 |
+* `anno_barplot()`: allows to add numbers on top of bars. |
|
| 10 | 11 |
|
| 11 | 12 |
========================= |
| 12 | 13 |
|
Zuguang Gu authored on 03/08/2021 08:49:11
| ... | ... |
@@ -5,6 +5,8 @@ CHANGES in VERSION 2.9.3 |
| 5 | 5 |
* set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects. |
| 6 | 6 |
* `make_comb_mat()`: support `GRangesList` object as input. |
| 7 | 7 |
* legends: fixed a bug of the grid heights were not correctedly calculated. |
| 8 |
+* discrete annotations: neighbour grids are merged into one single grid if they have the |
|
| 9 |
+ same values. |
|
| 8 | 10 |
|
| 9 | 11 |
========================= |
| 10 | 12 |
|
Zuguang Gu authored on 02/08/2021 19:42:49
| ... | ... |
@@ -4,6 +4,7 @@ CHANGES in VERSION 2.9.3 |
| 4 | 4 |
* throw error when the heatmaps (list) are already initialized by draw() when adding them. |
| 5 | 5 |
* set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects. |
| 6 | 6 |
* `make_comb_mat()`: support `GRangesList` object as input. |
| 7 |
+* legends: fixed a bug of the grid heights were not correctedly calculated. |
|
| 7 | 8 |
|
| 8 | 9 |
========================= |
| 9 | 10 |
|
Zuguang Gu authored on 02/08/2021 10:26:51
| ... | ... |
@@ -3,6 +3,7 @@ CHANGES in VERSION 2.9.3 |
| 3 | 3 |
* `pheatmap()`/`heatmap()`/`heatmap.2()`: set default of run_draw to FALSE. |
| 4 | 4 |
* throw error when the heatmaps (list) are already initialized by draw() when adding them. |
| 5 | 5 |
* set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects. |
| 6 |
+* `make_comb_mat()`: support `GRangesList` object as input. |
|
| 6 | 7 |
|
| 7 | 8 |
========================= |
| 8 | 9 |
|
Zuguang Gu authored on 26/07/2021 09:27:34
| ... | ... |
@@ -2,6 +2,7 @@ CHANGES in VERSION 2.9.3 |
| 2 | 2 |
|
| 3 | 3 |
* `pheatmap()`/`heatmap()`/`heatmap.2()`: set default of run_draw to FALSE. |
| 4 | 4 |
* throw error when the heatmaps (list) are already initialized by draw() when adding them. |
| 5 |
+* set `wrap = TRUE` in `grid.grabExpr()` when capturing the legend objects. |
|
| 5 | 6 |
|
| 6 | 7 |
========================= |
| 7 | 8 |
|
Zuguang Gu authored on 22/07/2021 20:35:41
| ... | ... |
@@ -1,8 +1,17 @@ |
| 1 |
+CHANGES in VERSION 2.9.3 |
|
| 2 |
+ |
|
| 3 |
+* `pheatmap()`/`heatmap()`/`heatmap.2()`: set default of run_draw to FALSE. |
|
| 4 |
+* throw error when the heatmaps (list) are already initialized by draw() when adding them. |
|
| 5 |
+ |
|
| 6 |
+========================= |
|
| 7 |
+ |
|
| 1 | 8 |
CHANGES in VERSION 2.9.2 |
| 2 | 9 |
|
| 3 | 10 |
* fixed a bug of `bg_col` for transposed matrix in `UpSet()`. |
| 4 | 11 |
* print warnings if names of annotations have different orders from the matrix row/column names. |
| 5 | 12 |
|
| 13 |
+========================= |
|
| 14 |
+ |
|
| 6 | 15 |
CHANGES in VERSION 2.9.1 |
| 7 | 16 |
|
| 8 | 17 |
* fixed a bug of editing gTree object where the list element "just" has been |
Zuguang Gu authored on 13/07/2021 15:43:05
Zuguang Gu authored on 03/07/2021 08:17:56
Zuguang Gu authored on 01/07/2021 11:29:17
| ... | ... |
@@ -1,3 +1,10 @@ |
| 1 |
+CHANGES in VERSION 2.9.1 |
|
| 2 |
+ |
|
| 3 |
+* fixed a bug of editing gTree object where the list element "just" has been |
|
| 4 |
+ changed to "justification" in recent R versions. |
|
| 5 |
+ |
|
| 6 |
+========================= |
|
| 7 |
+ |
|
| 1 | 8 |
CHANGES in VERSION 2.7.10 |
| 2 | 9 |
|
| 3 | 10 |
* `anno_simple()`: text symbols can have nchar > 1. |
Zuguang authored on 04/05/2021 13:55:58
Zuguang authored on 07/04/2021 08:47:30
Zuguang authored on 07/04/2021 08:20:24
Zuguang authored on 04/04/2021 13:30:00
Zuguang authored on 24/03/2021 09:05:20
Zuguang Gu authored on 11/03/2021 09:41:22
Zuguang Gu authored on 04/03/2021 09:51:27
Zuguang Gu authored on 09/02/2021 20:31:08
| ... | ... |
@@ -4,6 +4,7 @@ CHANGES in VERSION 2.7.7 |
| 4 | 4 |
* parallel is implemented with foreach + doParallel |
| 5 | 5 |
* expression is properly processed for discrete legends |
| 6 | 6 |
* `adjust_dend_by_x()`: simplified the representation of units. |
| 7 |
+* number of split can be the same as number of matrix rows/columns. |
|
| 7 | 8 |
|
| 8 | 9 |
========================== |
| 9 | 10 |
|
Zuguang Gu authored on 09/02/2021 19:57:24
| ... | ... |
@@ -3,6 +3,7 @@ CHANGES in VERSION 2.7.7 |
| 3 | 3 |
* discrete numeric legend labels are in correct order now. |
| 4 | 4 |
* parallel is implemented with foreach + doParallel |
| 5 | 5 |
* expression is properly processed for discrete legends |
| 6 |
+* `adjust_dend_by_x()`: simplified the representation of units. |
|
| 6 | 7 |
|
| 7 | 8 |
========================== |
| 8 | 9 |
|
Zuguang Gu authored on 09/02/2021 13:53:11
| ... | ... |
@@ -1,10 +1,12 @@ |
| 1 |
-CHANGES in VERSION 2.7.5 |
|
| 1 |
+CHANGES in VERSION 2.7.7 |
|
| 2 | 2 |
|
| 3 | 3 |
* discrete numeric legend labels are in correct order now. |
| 4 |
+* parallel is implemented with foreach + doParallel |
|
| 5 |
+* expression is properly processed for discrete legends |
|
| 4 | 6 |
|
| 5 | 7 |
========================== |
| 6 | 8 |
|
| 7 |
-CHANGES in VERSION 2.7.5 |
|
| 9 |
+CHANGES in VERSION 2.7.6 |
|
| 8 | 10 |
|
| 9 | 11 |
* `Legend()`: add a new argument `grob`. |
| 10 | 12 |
|
Zuguang Gu authored on 26/01/2021 16:10:51
Zuguang Gu authored on 24/01/2021 08:39:14
| ... | ... |
@@ -1,5 +1,11 @@ |
| 1 | 1 |
CHANGES in VERSION 2.7.5 |
| 2 | 2 |
|
| 3 |
+* `Legend()`: add a new argument `grob`. |
|
| 4 |
+ |
|
| 5 |
+========================== |
|
| 6 |
+ |
|
| 7 |
+CHANGES in VERSION 2.7.5 |
|
| 8 |
+ |
|
| 3 | 9 |
* `anno_block()`: add `labels_offset` and `labels_just`. |
| 4 | 10 |
* `anno_lines()`: `show_points` can be a vector. |
| 5 | 11 |
* `pheatmap()`: support `kmeans_k`. |
Zuguang Gu authored on 22/01/2021 10:25:28
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 22/01/2021 09:39:05
Zuguang Gu authored on 31/12/2020 09:02:28
Zuguang Gu authored on 14/12/2020 08:38:56
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 13/12/2020 20:54:51
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 01/12/2020 16:03:08
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 24/11/2020 08:23:47
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 22/11/2020 20:40:20
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 10/11/2020 10:56:48
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 10/11/2020 07:28:08
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 09/11/2020 22:29:27
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 02/11/2020 08:55:29
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 01/11/2020 08:44:36
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 30/10/2020 19:29:11
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 30/10/2020 15:10:21
| ... | ... |
@@ -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`. |
Zuguang Gu authored on 23/10/2020 16:02:23
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 23/10/2020 07:29:40
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 22/10/2020 10:44:27
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 21/10/2020 07:52:11
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 20/10/2020 19:30:27
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 20/10/2020 13:15:35
Zuguang Gu authored on 20/10/2020 07:36:13
Zuguang Gu authored on 14/10/2020 13:05:19
simplifyEnrichment authored on 13/10/2020 12:40:30
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 11/10/2020 18:24:04
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 09/10/2020 13:12:56
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 09/10/2020 07:50:19
| ... | ... |
@@ -7,6 +7,7 @@ CHANGES in VERSION 2.5.5 |
| 7 | 7 |
* `ht_opt$TITLE_PADDING` can be set with a unit of length two. |
| 8 | 8 |
* `HeatmapAnnotation()`: remove colors that are not in the annotations. |
| 9 | 9 |
* `pheatmap()`: fixed a bug when length(breaks) = length(color) + 1 |
| 10 |
+* `pheatmap()`: legend breaks are centered to zero if the matrix is scaled. |
|
| 10 | 11 |
|
| 11 | 12 |
====================== |
| 12 | 13 |
|
Zuguang Gu authored on 08/10/2020 19:11:38
| ... | ... |
@@ -6,6 +6,7 @@ CHANGES in VERSION 2.5.5 |
| 6 | 6 |
* `pheatmap()`: improve the setting of `color` and `breaks`. |
| 7 | 7 |
* `ht_opt$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 |
|
Zuguang Gu authored on 08/10/2020 08:44:52
| ... | ... |
@@ -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 |
|
simplifyEnrichment authored on 06/10/2020 12:07:17
| ... | ... |
@@ -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 |
|
simplifyEnrichment authored on 06/10/2020 08:38:50
Zuguang Gu authored on 30/09/2020 07:23:38
Zuguang Gu authored on 12/09/2020 12:12:16
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 09/09/2020 06:54:18
| ... | ... |
@@ -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 |
|
Zuguang Gu authored on 18/07/2020 08:35:54
Zuguang Gu authored on 10/07/2020 09:02:24
Zuguang Gu authored on 05/07/2020 20:11:01
Zuguang Gu authored on 02/07/2020 10:40:04
Zuguang Gu authored on 29/06/2020 15:54:31
Zuguang Gu authored on 28/06/2020 20:28:06
Zuguang Gu authored on 28/06/2020 13:14:25