1. ggtree
  2. NEWS.md
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fixed R check

Guangchuang Yu authored on 04/04/2023 03:12:42
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NEWS.md
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-# ggtree 3.7.1.003
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+# ggtree 3.7.2
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 + `ggtree()` supports 'dendro' object (`ggdendro::dendro_data()` output) (2023-03-02, Thu)
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 + update `theme_dendrogram()` to use `ggfun::theme_noxaxis()` (2022-11-21, Mon)
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ggtree supports dendro object

Guangchuang Yu authored on 02/03/2023 02:23:07
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NEWS.md
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-# ggtree 3.7.1.002
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+# ggtree 3.7.1.003
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++ `ggtree()` supports 'dendro' object (`ggdendro::dendro_data()` output) (2023-03-02, Thu)
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 + update `theme_dendrogram()` to use `ggfun::theme_noxaxis()` (2022-11-21, Mon)
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 + using `cli::cli_alert_warning()` instead of `warning_wrap` (2022-11-10, Thu)
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update theme_dendrogram

Guangchuang Yu authored on 21/11/2022 02:28:11
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NEWS.md
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-# ggtree 3.7.1.001
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+# ggtree 3.7.1.002
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++ update `theme_dendrogram()` to use `ggfun::theme_noxaxis()` (2022-11-21, Mon)
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 + using `cli::cli_alert_warning()` instead of `warning_wrap` (2022-11-10, Thu)
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 # ggtree 3.7.1
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update docs

Guangchuang Yu authored on 10/11/2022 10:01:17
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NEWS.md
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+# ggtree 3.7.1.001
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++ using `cli::cli_alert_warning()` instead of `warning_wrap` (2022-11-10, Thu)
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 # ggtree 3.7.1
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 + compatible with ggplot2 v=3.4.0 (2022-11-07, Mon)
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bump version

Guangchuang Yu authored on 06/11/2022 14:52:54
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NEWS.md
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-# ggtree 3.7.0.001
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+# ggtree 3.7.1
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++ compatible with ggplot2 v=3.4.0 (2022-11-07, Mon)
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 + allows setting `options(clade_align = TRUE)` to align `geom_hilight()` layer and allows setting `options(clade_width_extend = 0.35)` to set the amount the width extension (in y-axis) of `geom_hilight()`. These two features is designed for `ggtreeDendro::geom_rect_subtree()` layer (2022-11-06, Sun)
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 # ggtree 3.6.0
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geom_hilight options

Guangchuang Yu authored on 06/11/2022 07:48:45
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NEWS.md
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+# ggtree 3.7.0.001
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++ allows setting `options(clade_align = TRUE)` to align `geom_hilight()` layer and allows setting `options(clade_width_extend = 0.35)` to set the amount the width extension (in y-axis) of `geom_hilight()`. These two features is designed for `ggtreeDendro::geom_rect_subtree()` layer (2022-11-06, Sun)
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 # ggtree 3.6.0
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Browse code

update docs

Guangchuang Yu authored on 02/11/2022 02:53:13
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update

Guangchuang Yu authored on 26/09/2022 07:42:10
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NEWS.md
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-# ggtree 3.5.3.001
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+# ggtree 3.5.3.002
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++ add new citation (the iMeta 2022 paper) (2022-09-26, Mon)
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 + move `scale_color_subtree()` to the 'ggtreeDendro' package (2022-09-23, Fri)
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 # ggtree 3.5.3
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move scale-color-subtree to ggtreeDendro

Guangchuang Yu authored on 23/09/2022 02:52:18
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NEWS.md
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   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
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+
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+# ggtree 3.5.3.001
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++ move `scale_color_subtree()` to the 'ggtreeDendro' package (2022-09-23, Fri)
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 # ggtree 3.5.3
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 + update `fortify` method for `pvclust` object (2022-08-15, Mon)
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bump version

Guangchuang Yu authored on 19/08/2022 08:36:03
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NEWS.md
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   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
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-# ggtree 3.5.2.992
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+# ggtree 3.5.3
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 + update `fortify` method for `pvclust` object (2022-08-15, Mon)
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 + add citation of the tree data book (2022-08-13, Sat)
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update docs

Guangchuang Yu authored on 15/08/2022 10:06:17
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NEWS.md
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   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
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-# ggtree 3.5.2.991
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+# ggtree 3.5.2.992
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++ update `fortify` method for `pvclust` object (2022-08-15, Mon)
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 + add citation of the tree data book (2022-08-13, Sat)
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 # ggtree 3.5.2
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update citation

Guangchuang Yu authored on 13/08/2022 09:45:00
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   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
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+# ggtree 3.5.2.991
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+
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++ add citation of the tree data book (2022-08-13, Sat)
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 # ggtree 3.5.2
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Browse code

linkage support

Guangchuang Yu authored on 11/08/2022 09:03:41
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NEWS.md
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-# ggtree 3.5.1.902
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+# ggtree 3.5.2
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++ `scale_color_subtree()` now supports passing a numeric value and internally it will call `cutree(tree, k)` (2022-08-11, Thu)
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++ support 'linkage' class defined in the 'mdendro' package (2022-08-11, Thu)
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 + clone the plot environment before assigning layout (2022-07-19, Tue, #516)
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 + bug fixed in 'equal_angle' layout (2022-07-08, Fri, #514)
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 + optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu, #508)
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update docs

Guangchuang Yu authored on 19/07/2022 03:13:41
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NEWS.md
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-# ggtree 3.5.1.901
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++ clone the plot environment before assigning layout (2022-07-19, Tue, #516)
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 + bug fixed in 'equal_angle' layout (2022-07-08, Fri, #514)
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-+ optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu)
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++ optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu, #508)
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 # ggtree 3.5.1
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Browse code

update

Guangchuang Yu authored on 09/07/2022 07:33:16
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NEWS.md
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-# ggtree 3.5.1.900
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++ bug fixed in 'equal_angle' layout (2022-07-08, Fri, #514)
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 + optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu)
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 # ggtree 3.5.1
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update docs

Guangchuang Yu authored on 23/06/2022 03:18:21
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NEWS.md
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+# ggtree 3.5.1.900
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++ optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu)
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 # ggtree 3.5.1
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 + `as.phylo.hclust2` to correct edge length as displayed in `stats:::plot.hclust` (2022-06-21, Tue)
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as.phylo.hclust2

Guangchuang Yu authored on 21/06/2022 08:59:44
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NEWS.md
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-# ggtree 3.5.0.902
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+# ggtree 3.5.1
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++ `as.phylo.hclust2` to correct edge length as displayed in `stats:::plot.hclust` (2022-06-21, Tue)
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 + add outline to nodepies (2022-06-20, Mon, #506)
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-+ `update_edge_hclust()` to adjust edge length of a `phylo` object converted from a `hclust` object via `ape::as.phylo()` (2022-06-05, Sun)
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 + new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497)
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     - only works for Cartesian coordination, that means it will not work for `layout = 'radial'`
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Browse code

update

Guangchuang Yu authored on 20/06/2022 07:13:19
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NEWS.md
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-# ggtree 3.5.0.901
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+# ggtree 3.5.0.902
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++ add outline to nodepies (2022-06-20, Mon, #506)
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 + `update_edge_hclust()` to adjust edge length of a `phylo` object converted from a `hclust` object via `ape::as.phylo()` (2022-06-05, Sun)
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 + new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497)
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     - only works for Cartesian coordination, that means it will not work for `layout = 'radial'`
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update_edge_hclust

Guangchuang Yu authored on 04/06/2022 17:02:02
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NEWS.md
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-# ggtree 3.5.0.900
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+# ggtree 3.5.0.901
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++ `update_edge_hclust()` to adjust edge length of a `phylo` object converted from a `hclust` object via `ape::as.phylo()` (2022-06-05, Sun)
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 + new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497)
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     - only works for Cartesian coordination, that means it will not work for `layout = 'radial'`
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Browse code

update docs, #496, #497

Guangchuang Yu authored on 29/04/2022 08:02:38
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NEWS.md
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+# ggtree 3.5.0.900
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++ new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497)
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+    - only works for Cartesian coordination, that means it will not work for `layout = 'radial'`
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+
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+# ggtree 3.4.0
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+
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++ Bioconductor 3.15 release (2022-04-28, Thu)
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+
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 # ggtree 3.3.3
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 + `geom_striplab()` that supports `aes()` mapping (2022-04-22, Fri, #493)
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bump version

Guangchuang Yu authored on 24/04/2022 02:10:02
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NEWS.md
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+# ggtree 3.3.3
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+
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++ `geom_striplab()` that supports `aes()` mapping (2022-04-22, Fri, #493)
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++ `to.bottom` parameter introduced in `geom_hilight()` to allow the highlight layer was added into the lowest layer stack (2022-04-22, Fri, #492)
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+
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 # ggtree 3.3.2
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 + mv `identify()` method to 'ggfun' (2022-04-01, Fri)
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bump version

Guangchuang Yu authored on 14/04/2022 01:47:54
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-# ggtree 3.3.1.901
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+# ggtree 3.3.2
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 + mv `identify()` method to 'ggfun' (2022-04-01, Fri)
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 + update `identify.gg()` to support 'ggplot' object and `+xlim()`
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mv identify to ggfun

Guangchuang Yu authored on 01/04/2022 08:21:52
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 # ggtree 3.3.1.901
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-+ update `identify.gg()` to support 'ggplot' object and `+xlim()` (2022-04-01, Fri)
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++ mv `identify()` method to 'ggfun' (2022-04-01, Fri)
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++ update `identify.gg()` to support 'ggplot' object and `+xlim()`
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 + update man files (2022-03-23, Wed, #489)
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 # ggtree 3.3.1
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update identify() method

Guangchuang Yu authored on 01/04/2022 02:45:58
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NEWS.md
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-# ggtree 3.3.1.900
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+# ggtree 3.3.1.901
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++ update `identify.gg()` to support 'ggplot' object and `+xlim()` (2022-04-01, Fri)
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 + update man files (2022-03-23, Wed, #489)
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 # ggtree 3.3.1
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update man files and fixed R check

Guangchuang Yu authored on 23/03/2022 04:13:34
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NEWS.md
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   - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo>
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 + `fortify` method for `phyloseq` object should return a tidy data.frame
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   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`
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-+ update ggtree man files
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 + The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
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   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
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+# ggtree 3.3.1.900
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++ update man files (2022-03-23, Wed, #489)
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 # ggtree 3.3.1
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 + use graph layouts to visualize tree (2021-12-10, Fri, #460, #461)
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bump version

Guangchuang Yu authored on 10/12/2021 09:53:25
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NEWS.md
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 # TODO LIST
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-+ use graph layout to visualize tree
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-  - <https://github.com/YuLab-SMU/ggtree/issues/460>
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-    + igraph layout
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-    + graphlayouts: <https://cran.r-project.org/web/packages/graphlayouts/index.html>
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-    + TreeAndLeaf layout: <https://www.bioconductor.org/packages/TreeAndLeaf>
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+
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++ TreeAndLeaf layout: <https://www.bioconductor.org/packages/TreeAndLeaf>
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 + `phylogeography`
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   - <https://stackoverflow.com/questions/68668788/phylogeography-how-to-combine-phylogenetic-tree-and-geographic-map-and-create>
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 + `phylomorphospace`
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-# ggtree 3.3.0.901
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-
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+# ggtree 3.3.1
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+
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++ use graph layouts to visualize tree (2021-12-10, Fri, #460, #461)
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+  - igraph layout
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+  - graphlayouts: <https://cran.r-project.org/web/packages/graphlayouts/index.html>
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 + `scale_color_subtree` and `scale_colour_subtree` to color subtree via taxa group information (e.g., cutree, or kmeans) (2021-12-01, Wed)
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 + set `na.value = 'white'` in `msaplot()` (2021-10-29, Fri)
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Browse code

Update NEWS.md

Guangchuang Yu authored on 08/12/2021 15:52:15 • GitHub committed on 08/12/2021 15:52:15
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NEWS.md
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 # TODO LIST
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++ use graph layout to visualize tree
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+  - <https://github.com/YuLab-SMU/ggtree/issues/460>
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+    + igraph layout
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+    + graphlayouts: <https://cran.r-project.org/web/packages/graphlayouts/index.html>
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+    + TreeAndLeaf layout: <https://www.bioconductor.org/packages/TreeAndLeaf>
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 + `phylogeography`
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   - <https://stackoverflow.com/questions/68668788/phylogeography-how-to-combine-phylogenetic-tree-and-geographic-map-and-create>
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 + `phylomorphospace`
Browse code

direct support kmeans

Guangchuang Yu authored on 02/12/2021 03:27:15
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 # ggtree 3.3.0.901
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-+ `scale_color_subtree` and `scale_colour_subtree` to color subtree via taxa group information (e.g., cutree) (2021-12-01, Wed)
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++ `scale_color_subtree` and `scale_colour_subtree` to color subtree via taxa group information (e.g., cutree, or kmeans) (2021-12-01, Wed)
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 + set `na.value = 'white'` in `msaplot()` (2021-10-29, Fri)
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 # ggtree 3.2.0
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scale_color_subtree

Guangchuang Yu authored on 01/12/2021 08:14:20
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-# ggtree 3.3.0.900
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+# ggtree 3.3.0.901
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++ `scale_color_subtree` and `scale_colour_subtree` to color subtree via taxa group information (e.g., cutree) (2021-12-01, Wed)
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 + set `na.value = 'white'` in `msaplot()` (2021-10-29, Fri)
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 # ggtree 3.2.0
Browse code

todo

Guangchuang Yu authored on 15/11/2021 02:29:43
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 # TODO LIST
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++ `phylogeography`
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+  - <https://stackoverflow.com/questions/68668788/phylogeography-how-to-combine-phylogenetic-tree-and-geographic-map-and-create>
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 + `phylomorphospace`
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   - <https://github.com/YuLab-SMU/ggtree/issues/370>
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   - <https://github.com/wabarr/ggphylomorpho>
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todo

Guangchuang Yu authored on 12/11/2021 05:44:12
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 # TODO LIST
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 + `phylomorphospace`
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-+ `type` parameter in `geom_hilight` accepts 'roundrect' and 'gradient'
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-  - <https://github.com/YuLab-SMU/ggtree/pull/444#issuecomment-949335277>
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+  - <https://github.com/YuLab-SMU/ggtree/issues/370>
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+  - <https://github.com/wabarr/ggphylomorpho>
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++ visualize support values obtained from different methods
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+  - <https://github.com/YuLab-SMU/ggtree/issues/451>
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 + `height` parameter to `collapse()`
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   - <https://github.com/YuLab-SMU/ggtree/issues/409#issuecomment-944034311>
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 + rewrite `revts` to `scale_revts`
Browse code

phylomorphospace

Guangchuang Yu authored on 08/11/2021 01:34:55
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 # TODO LIST
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++ `phylomorphospace`
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   - <https://github.com/YuLab-SMU/ggtree/pull/444#issuecomment-949335277>
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 + `height` parameter to `collapse()`
Browse code

set na.value="white" in msaplot()

Guangchuang Yu authored on 29/10/2021 08:09:56
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+# ggtree 3.3.0.900
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++ set `na.value = 'white'` in `msaplot()` (2021-10-29, Fri)
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+
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+# ggtree 3.2.0
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+
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++ Bioconductor 3.14 release
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 # ggtree 3.1.6
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Browse code

update news

Guangchuang Yu authored on 25/10/2021 04:05:37
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NEWS.md
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 # TODO LIST
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++ `type` parameter in `geom_hilight` accepts 'roundrect' and 'gradient'
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+  - <https://github.com/YuLab-SMU/ggtree/pull/444#issuecomment-949335277>
5 7 
 + `height` parameter to `collapse()`
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   - <https://github.com/YuLab-SMU/ggtree/issues/409#issuecomment-944034311>
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 + rewrite `revts` to `scale_revts`
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21 23 
 # ggtree 3.1.6
22 24
23 25 
 + `geom_cladelab` now supports extend parameter as in `geom_cladelabel` (2021-10-14, Thu, @xiangpin, #446)
24 
-+ `geom_hilight` supports fill linear gradient colour and round rect background (2021-10-11, Mon; @xiangpin, #444)
26 
++ `geom_hilight` supports fill linear gradient colour and round rect background (2021-10-11, Mon; @xiangpin, #449, #444)
25 27 
 + work with negative edge lengths (`hclust` may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441, #445)
26 28
27 29 
 # ggtree 3.1.5
Browse code

Merge branch 'master' of github.com:YuLab-SMU/ggtree

Guangchuang Yu authored on 20/10/2021 03:11:29
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bump version

Guangchuang Yu authored on 20/10/2021 03:09:01
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 -->
20 20
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-# ggtree 3.1.5.902
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+# ggtree 3.1.6
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24 24 
 + `geom_cladelab` now supports extend parameter as in `geom_cladelabel` (2021-10-14, Thu, @xiangpin, #446)
25 25 
 + `geom_hilight` supports fill linear gradient colour and round rect background (2021-10-11, Mon; @xiangpin, #444)
Browse code

Update NEWS.md

Guangchuang Yu authored on 15/10/2021 06:32:02 • GitHub committed on 15/10/2021 06:32:02
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 + `height` parameter to `collapse()`
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   - <https://github.com/YuLab-SMU/ggtree/issues/409#issuecomment-944034311>
7 
++ rewrite `revts` to `scale_revts`
8 
++ `inset` and relative functions support circular layout
7 9 
 + tanglegram support
8 10 
   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
9 11 
   - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo>
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12 14 
 + update ggtree man files
13 15 
 + The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
14 16 
   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
15 
-+ rewrite `revts` to `scale_revts`
16 
-+ `geom_hilight` supports linear gradual colored rectangle
17 
-  - e.g., `grid.rect(gp=gpar(fill=linearGradient()))`
18 
-  - <https://developer.r-project.org/Blog/public/2020/07/15/new-features-in-the-r-graphics-engine/>
19 
-+ `inset` and relative functions support circular layout
20 17
21 18 
 -->
22 19
Browse code

Update NEWS.md

Guangchuang Yu authored on 15/10/2021 06:25:49 • GitHub committed on 15/10/2021 06:25:49
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NEWS.md
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@@ -2,6 +2,8 @@
2 2
3 3 
 # TODO LIST
4 4
5 
++ `height` parameter to `collapse()`
6 
+  - <https://github.com/YuLab-SMU/ggtree/issues/409#issuecomment-944034311>
5 7 
 + tanglegram support
6 8 
   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
7 9 
   - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo>
Browse code

update news

Guangchuang Yu authored on 14/10/2021 01:59:58
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1 
+<!--
2 
+
1 3 
 # TODO LIST
2 4
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 + tanglegram support
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12 14 
 + `geom_hilight` supports linear gradual colored rectangle
13 15 
   - e.g., `grid.rect(gp=gpar(fill=linearGradient()))`
14 16 
   - <https://developer.r-project.org/Blog/public/2020/07/15/new-features-in-the-r-graphics-engine/>
17 
++ `inset` and relative functions support circular layout
18 
+
19 
+-->
15 20
16 21
17 
-# ggtree 3.1.5.901
22 
+# ggtree 3.1.5.902
18 23
24 
++ `geom_cladelab` now supports extend parameter as in `geom_cladelabel` (2021-10-14, Thu, @xiangpin, #446)
19 25 
 + `geom_hilight` supports fill linear gradient colour and round rect background (2021-10-11, Mon; @xiangpin, #444)
20 26 
 + work with negative edge lengths (`hclust` may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441, #445)
21 27
Browse code

update docs

Guangchuang Yu authored on 12/10/2021 08:54:53
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14 14 
   - <https://developer.r-project.org/Blog/public/2020/07/15/new-features-in-the-r-graphics-engine/>
15 15
16 16
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-# ggtree 3.1.5.900
17 
+# ggtree 3.1.5.901
18 18
19 
-+ work with negative edge lengths (`hclust` may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441)
19 
++ `geom_hilight` supports fill linear gradient colour and round rect background (2021-10-11, Mon; @xiangpin, #444)
20 
++ work with negative edge lengths (`hclust` may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441, #445)
20 21
21 22 
 # ggtree 3.1.5
22 23
Browse code

todo

Guangchuang Yu authored on 05/10/2021 06:16:49
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@@ -9,6 +9,10 @@
9 9 
 + The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
10 10 
   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
11 11 
 + rewrite `revts` to `scale_revts`
12 
++ `geom_hilight` supports linear gradual colored rectangle
13 
+  - e.g., `grid.rect(gp=gpar(fill=linearGradient()))`
14 
+  - <https://developer.r-project.org/Blog/public/2020/07/15/new-features-in-the-r-graphics-engine/>
15 
+
12 16
13 17 
 # ggtree 3.1.5.900
14 18
Browse code

update docs

Guangchuang Yu authored on 29/09/2021 07:39:23
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10 10 
   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
11 11 
 + rewrite `revts` to `scale_revts`
12 12
13 
+# ggtree 3.1.5.900
14 
+
15 
++ work with negative edge lengths (`hclust` may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441)
13 16
14 17 
 # ggtree 3.1.5
15 18
Browse code

bump version

Guangchuang Yu authored on 28/09/2021 02:28:22
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11 11 
 + rewrite `revts` to `scale_revts`
12 12
13 13
14 
-# ggtree 3.1.4.993
14 
+# ggtree 3.1.5
15 15
16 
-+ `ggdensitree` with `align.tips=TRUE` sets max x to 0 (2021-09-26, Sun, @brj1, #439)
16 
++ `ggdensitree` with `align.tips=TRUE` sets max x to 0 (2021-09-26, Sun; @brj1, #437, #439)
17 17 
 + custom column headers for `gheatmap` (2021-09-15, Wed, @matt-sd-watson, #434)
18 18 
 + bug fixed of `nudge_x` parameter in `geom_segment2` (2021-09-03, Fri; @xiangpin, #433)
19 19
Browse code

update docs

Guangchuang Yu authored on 27/09/2021 01:45:34
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1 
-# ggtree 3.1.4.992
1 
+# TODO LIST
2 2
3 
++ tanglegram support
4 
+  - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
5 
+  - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo>
6 
++ `fortify` method for `phyloseq` object should return a tidy data.frame
7 
+  - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`
8 
++ update ggtree man files
9 
++ The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
10 
+  - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
11 
++ rewrite `revts` to `scale_revts`
12 
+
13 
+
14 
+# ggtree 3.1.4.993
15 
+
16 
++ `ggdensitree` with `align.tips=TRUE` sets max x to 0 (2021-09-26, Sun, @brj1, #439)
3 17 
 + custom column headers for `gheatmap` (2021-09-15, Wed, @matt-sd-watson, #434)
4 18 
 + bug fixed of `nudge_x` parameter in `geom_segment2` (2021-09-03, Fri; @xiangpin, #433)
5 19
Browse code

fixed R check

Guangchuang Yu authored on 15/09/2021 02:29:08
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1 
-# ggtree 3.1.4.991
1 
+# ggtree 3.1.4.992
2 2
3 
++ custom column headers for `gheatmap` (2021-09-15, Wed, @matt-sd-watson, #434)
3 4 
 + bug fixed of `nudge_x` parameter in `geom_segment2` (2021-09-03, Fri; @xiangpin, #433)
4 5
5 6 
 # ggtree 3.1.4
Browse code

update docs

Guangchuang Yu authored on 03/09/2021 08:47:25
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1 
+# ggtree 3.1.4.991
2 
+
3 
++ bug fixed of `nudge_x` parameter in `geom_segment2` (2021-09-03, Fri; @xiangpin, #433)
4 
+
1 5 
 # ggtree 3.1.4
2 6
3 7 
 + introduce `align` parameter in `geom_hilight` (2021-08-30, Mon; @xiangpin, #431)
Browse code

bump version

Guangchuang Yu authored on 30/08/2021 07:41:48
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NEWS.md
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1 
-# ggtree 3.1.3.993
1 
+# ggtree 3.1.4
2 2
3 
++ introduce `align` parameter in `geom_hilight` (2021-08-30, Mon; @xiangpin, #431)
3 4 
 + the `data` parameter in `geom_facet` now accepts function as input (2021-08-22, Sun; @xiangpin, #430)
4 5 
 + import `ggfun` and `yulab.utils` (2021-08-20, Fri)
5 6 
 + allow using `options(layout.radial.linetype)` to set linetype of radial layout (either 'strainght' or 'curved') (2021-08-13, Fri; @xiangpin, #427)
Browse code

update docs

Guangchuang Yu authored on 22/08/2021 03:57:17
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-# ggtree 3.1.3.992
1 
+# ggtree 3.1.3.993
2 2
3 
++ the `data` parameter in `geom_facet` now accepts function as input (2021-08-22, Sun; @xiangpin, #430)
3 4 
 + import `ggfun` and `yulab.utils` (2021-08-20, Fri)
4 5 
 + allow using `options(layout.radial.linetype)` to set linetype of radial layout (either 'strainght' or 'curved') (2021-08-13, Fri; @xiangpin, #427)
5 6
Browse code

update docs

Guangchuang Yu authored on 20/08/2021 07:12:33
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1 
-# ggtree 3.1.3.991
1 
+# ggtree 3.1.3.992
2 2
3 
++ import `ggfun` and `yulab.utils` (2021-08-20, Fri)
3 4 
 + allow using `options(layout.radial.linetype)` to set linetype of radial layout (either 'strainght' or 'curved') (2021-08-13, Fri; @xiangpin, #427)
4 5
5 6 
 # ggtree 3.1.3
Browse code

update docs

Guangchuang Yu authored on 14/08/2021 09:09:12
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+# ggtree 3.1.3.991
2 
+
3 
++ allow using `options(layout.radial.linetype)` to set linetype of radial layout (either 'strainght' or 'curved') (2021-08-13, Fri; @xiangpin, #427)
4 
+
1 5 
 # ggtree 3.1.3
2 6
3 7 
 + `data` argument in `geom_tiplab` and `position` argument in `geom_tree` (2021-08-10, Tue; #426, @xiangpin)
Browse code

bump up version

Guangchuang Yu authored on 10/08/2021 08:59:12
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NEWS.md
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1 
-# ggtree 3.1.2.992
1 
+# ggtree 3.1.3
2 2
3 
++ `data` argument in `geom_tiplab` and `position` argument in `geom_tree` (2021-08-10, Tue; #426, @xiangpin)
3 4 
 + `geom_hilight` and `geom_cladelab` supports function as input data (2021-07-28, Wed; #421, @xiangpin)
4 5 
 + `td_mutate` for mutating tree data
5 6 
 + `geom_tiplab` supports fontface aesthetic (2021-07-06, Tue; @xiangpin)
Browse code

update docs

Guangchuang Yu authored on 28/07/2021 07:35:07
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-# ggtree 3.1.2.991
1 
+# ggtree 3.1.2.992
2 2
3 
++ `geom_hilight` and `geom_cladelab` supports function as input data (2021-07-28, Wed; #421, @xiangpin)
4 
++ `td_mutate` for mutating tree data
3 5 
 + `geom_tiplab` supports fontface aesthetic (2021-07-06, Tue; @xiangpin)
4 6
5 7 
 # ggtree 3.1.2
Browse code

update news

Guangchuang Yu authored on 06/07/2021 13:15:54
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1 
+# ggtree 3.1.2.991
2 
+
3 
++ `geom_tiplab` supports fontface aesthetic (2021-07-06, Tue; @xiangpin)
4 
+
1 5 
 # ggtree 3.1.2
2 6
3 7 
 + calculate branch mid point for unrooted layout tree (2021-06-11, Fri)
Browse code

bump version up

Guangchuang Yu authored on 21/06/2021 02:21:27
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-# ggtree 3.1.1.992
1 
+# ggtree 3.1.2
2 2
3 3 
 + calculate branch mid point for unrooted layout tree (2021-06-11, Fri)
4 4 
   - `branch.y` and `branch.x`
Browse code

update docs

Guangchuang Yu authored on 11/06/2021 09:02:22
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NEWS.md
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1 
-# ggtree 3.1.1.991
1 
+# ggtree 3.1.1.992
2 2
3 
++ calculate branch mid point for unrooted layout tree (2021-06-11, Fri)
4 
+  - `branch.y` and `branch.x`
3 5 
 + `geom_range` supports aes mapping (2021-06-04, Fri)
4 6
5 7 
 # ggtree 3.1.1
Browse code

update docs

Guangchuang Yu authored on 04/06/2021 07:24:02
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NEWS.md
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1 
+# ggtree 3.1.1.991
2 
+
3 
++ `geom_range` supports aes mapping (2021-06-04, Fri)
4 
+
1 5 
 # ggtree 3.1.1
2 6
3 7 
 + bug fixed in `geom_range` (2021-06-01, Tue)
Browse code

bug fixed

Guangchuang Yu authored on 01/06/2021 09:22:43
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1 
-# ggtree 3.1.0.991
1 
+# ggtree 3.1.1
2 2
3 
++ bug fixed in `geom_range` (2021-06-01, Tue)
4 
+  - <https://github.com/YuLab-SMU/ggtree/pull/410>
3 5 
 + now `geom_nodelab` has a `node="internal"` parameter. (2021-05-31, Mon)
4 6 
   - if `node = "external"`, it equivalent to `geom_tiplab
5 7 
   - if `node = "all"`, it equivalent to `list(geom_tiplab(), geom_nodelab())`
Browse code

update docs

Guangchuang Yu authored on 01/06/2021 02:25:38
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1 
+# ggtree 3.1.0.991
2 
+
3 
++ now `geom_nodelab` has a `node="internal"` parameter. (2021-05-31, Mon)
4 
+  - if `node = "external"`, it equivalent to `geom_tiplab
5 
+  - if `node = "all"`, it equivalent to `list(geom_tiplab(), geom_nodelab())`
6 
+
7 
+# ggtree 3.0.0
8 
+
9 
++ Bioconductor 3.13 relese
10 
+
1 11 
 # ggtree 2.5.3
12 
+
2 13 
 + optimize text angle in `geom_cladelab` (2021-05-10, Mon)
3 14 
   - <https://github.com/YuLab-SMU/ggtree/pull/396>
4 15
Browse code

bump version

Guangchuang Yu authored on 10/05/2021 04:27:52
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NEWS.md
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1 
+# ggtree 2.5.3
2 
++ optimize text angle in `geom_cladelab` (2021-05-10, Mon)
3 
+  - <https://github.com/YuLab-SMU/ggtree/pull/396>
4 
+
1 5 
 # ggtree 2.5.2
2 6
3 7 
 + extend 'continuous' parameter to support 4 possible values, i.e., 'none' to disable continuous transition,  'color' (or 'colour') to enable continuous color transition, 'size' to enable continuous size (branch thickness) transition and 'all' to enable continuous color and size transition (2021-04-07, Wed)
Browse code

update docs

Guangchuang Yu authored on 07/04/2021 08:44:10
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-# ggtree 2.5.1.9002
1 
+# ggtree 2.5.2
2 2
3 
-+ 'inhibit.size' argument introduced to control whether 'continuous' parameter applies to color or both color and size (2021-03-30, Tue)
3 
++ extend 'continuous' parameter to support 4 possible values, i.e., 'none' to disable continuous transition,  'color' (or 'colour') to enable continuous color transition, 'size' to enable continuous size (branch thickness) transition and 'all' to enable continuous color and size transition (2021-04-07, Wed)
4 4 
   - <https://github.com/YuLab-SMU/ggtree/pull/385>
5 
+  - <https://github.com/YuLab-SMU/ggtree/pull/387>
5 6 
 + `extendto` argument for `geom_hilight` now compatible with 'inward_circular' and 'dendrogram' layouts (2021-02-25, Thu)
6 7 
   - <https://github.com/YuLab-SMU/ggtree/pull/379>
7 8
Browse code

update news

Guangchuang Yu authored on 30/03/2021 04:10:17
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-# ggtree 2.5.1.9001
1 
+# ggtree 2.5.1.9002
2 2
3 
++ 'inhibit.size' argument introduced to control whether 'continuous' parameter applies to color or both color and size (2021-03-30, Tue)
4 
+  - <https://github.com/YuLab-SMU/ggtree/pull/385>
3 5 
 + `extendto` argument for `geom_hilight` now compatible with 'inward_circular' and 'dendrogram' layouts (2021-02-25, Thu)
4 6 
   - <https://github.com/YuLab-SMU/ggtree/pull/379>
5 7
Browse code

update docs

Guangchuang Yu authored on 25/02/2021 01:54:42
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+# ggtree 2.5.1.9001
2 
+
3 
++ `extendto` argument for `geom_hilight` now compatible with 'inward_circular' and 'dendrogram' layouts (2021-02-25, Thu)
4 
+  - <https://github.com/YuLab-SMU/ggtree/pull/379>
5 
+
1 6 
 # ggtree 2.5.1
2 7
3 8 
 + update man file of `geom_rootpoint` (2021-01-08, Fri)
Browse code

v2.5.1

Guangchuang Yu authored on 08/01/2021 07:39:52
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-# ggtree 2.5.0.993
1 
+# ggtree 2.5.1
2 2
3 3 
 + update man file of `geom_rootpoint` (2021-01-08, Fri)
4 4 
 + `label` and `offset.label` introduced in `geom_treescale` layer (2020-12-23, Wed)
Browse code

update

Guangchuang Yu authored on 08/01/2021 07:30:55
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1 1 
 # ggtree 2.5.0.993
2 2
3 
++ update man file of `geom_rootpoint` (2021-01-08, Fri)
3 4 
 + `label` and `offset.label` introduced in `geom_treescale` layer (2020-12-23, Wed)
4 5 
   - <https://github.com/YuLab-SMU/ggtree/pull/360>
5 6 
 + `geom_rootedge` supports reversed x (2020-12-17, Thu)
Browse code

update news

Guangchuang Yu authored on 23/12/2020 01:12:44
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-# ggtree 2.5.0.992
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+# ggtree 2.5.0.993
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++ `label` and `offset.label` introduced in `geom_treescale` layer (2020-12-23, Wed)
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+  - <https://github.com/YuLab-SMU/ggtree/pull/360>
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++ `geom_rootedge` supports reversed x (2020-12-17, Thu)
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+  - <https://github.com/YuLab-SMU/ggtree/pull/358>
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 + `geom_nodelab()` now supports circular layout (2020-11-26, Thu)
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   - <https://github.com/YuLab-SMU/ggtree/issues/352>
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   - <https://github.com/YuLab-SMU/ggtree/pull/353>
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update docs

Guangchuang Yu authored on 26/11/2020 06:52:14
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-# ggtree 2.5.0.991
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+# ggtree 2.5.0.992
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++ `geom_nodelab()` now supports circular layout (2020-11-26, Thu)
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+  - <https://github.com/YuLab-SMU/ggtree/issues/352>
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+  - <https://github.com/YuLab-SMU/ggtree/pull/353>
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 + branch size can be grandualy changed (2020-10-29, Thu)
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   - <https://github.com/YuLab-SMU/ggtree/pull/349>
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Browse code

update url

Guangchuang Yu authored on 13/11/2020 14:29:27
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 + branch size can be grandualy changed (2020-10-29, Thu)
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   - <https://github.com/YuLab-SMU/ggtree/pull/349>
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+
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 # ggtree 2.4.0
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 + Bioconductor 3.12 release (2020-10-28, Wed)
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bump version

Guangchuang Yu authored on 29/10/2020 00:40:31
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+# ggtree 2.5.0.991
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+
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++ branch size can be grandualy changed (2020-10-29, Thu)
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+  - <https://github.com/YuLab-SMU/ggtree/pull/349>
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+
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 # ggtree 2.4.0
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 + Bioconductor 3.12 release (2020-10-28, Wed)
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new release

Guangchuang Yu authored on 28/10/2020 00:32:17
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+# ggtree 2.4.0
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++ Bioconductor 3.12 release (2020-10-28, Wed)
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+
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 # ggtree 2.3.7
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 + add `label_pad()` function to add padding characters to taxa labels (2020-10-09, Fri)
Browse code

bump up version

Guangchuang Yu authored on 10/10/2020 08:11:20
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-# ggtree 2.3.6.991
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+# ggtree 2.3.7
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 + add `label_pad()` function to add padding characters to taxa labels (2020-10-09, Fri)
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   - <https://groups.google.com/g/bioc-ggtree/c/INJ0Nfkq3b0/m/lXefnfV5AQAJ>
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label_pad

Guangchuang Yu authored on 09/10/2020 15:27:38
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+# ggtree 2.3.6.991
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+
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++ add `label_pad()` function to add padding characters to taxa labels (2020-10-09, Fri)
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+  - <https://groups.google.com/g/bioc-ggtree/c/INJ0Nfkq3b0/m/lXefnfV5AQAJ>
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++ add `family` parameter to `geom_tiplab()`
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+
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 # ggtree 2.3.6
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 + new layouts, `roundrect` and `ellipse`
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bump version up

Guangchuang Yu authored on 09/10/2020 03:09:26
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-# ggtree 2.3.5.993
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++ new layouts, `roundrect` and `ellipse`
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+  - <https://github.com/YuLab-SMU/ggtree/pull/344>
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+  - <https://github.com/YuLab-SMU/ggtree/pull/346>
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 + `fortify()` method for `treedataList` object (2020-09-20, Sun)
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 + `vexpand()` and `ggexpand()` to expand plot limit by ratio of plot range (2020-09-18, Fri)
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 + `geom_cladelab()`, an updated version of `geom_cladelabel` that supports aes mapping (2020-09-17, Thu)
Browse code

fortify method for treedataList

Guangchuang Yu authored on 20/09/2020 06:49:31
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-# ggtree 2.3.5.992
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+# ggtree 2.3.5.993
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++ `fortify()` method for `treedataList` object (2020-09-20, Sun)
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 + `vexpand()` and `ggexpand()` to expand plot limit by ratio of plot range (2020-09-18, Fri)
4 5 
 + `geom_cladelab()`, an updated version of `geom_cladelabel` that supports aes mapping (2020-09-17, Thu)
5 6 
   - <https://github.com/YuLab-SMU/ggtree/pull/342>
Browse code

ggexpand

Guangchuang Yu authored on 18/09/2020 08:19:27
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-# ggtree 2.3.5.991
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+# ggtree 2.3.5.992
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-+ `geom_cladelab`, an updated version of `geom_cladelabel` that supports aes mapping (2020-09-17, Thu)
3 
++ `vexpand()` and `ggexpand()` to expand plot limit by ratio of plot range (2020-09-18, Fri)
4 
++ `geom_cladelab()`, an updated version of `geom_cladelabel` that supports aes mapping (2020-09-17, Thu)
4 5 
   - <https://github.com/YuLab-SMU/ggtree/pull/342>
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 # ggtree 2.3.5
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update docs

Guangchuang Yu authored on 17/09/2020 01:45:18
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+# ggtree 2.3.5.991
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+
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++ `geom_cladelab`, an updated version of `geom_cladelabel` that supports aes mapping (2020-09-17, Thu)
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+  - <https://github.com/YuLab-SMU/ggtree/pull/342>
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+
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 # ggtree 2.3.5
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 + `td_unnest()` which return a function to flatten ggtree plot data (2020-09-14, Mon)
Browse code

td_unnest

Guangchuang Yu authored on 14/09/2020 02:14:03
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-# ggtree 2.3.4.993
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+# ggtree 2.3.5
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++ `td_unnest()` which return a function to flatten ggtree plot data (2020-09-14, Mon)
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+  - <https://yulab-smu.top/treedata-book/chapter12.html#td_unnest>
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 + update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)
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 + Defunct `geom_nodelab2()` (2020-09-02, Wed)
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 + `geom_tiplab()` and `geom_nodelab()` support `geom = "shadowtext"`
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-+ `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
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++ `td_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
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+  - <https://yulab-smu.top/treedata-book/chapter12.html#td_filter>
7 10 
 + update man files of `geom_rootedge` and `geom_point2`
8 11 
 + update `geom_hilight` to support `geom_hilight(data = tbl_tree, node = selected_node)`. (2020-09-03, Thu)
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update docs

Guangchuang Yu authored on 03/09/2020 02:53:24
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-# ggtree 2.3.4.992
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++ update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)
3 4 
 + Defunct `geom_nodelab2()` (2020-09-02, Wed)
4 5 
 + `geom_tiplab()` and `geom_nodelab()` support `geom = "shadowtext"`
5 6 
 + `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
Browse code

update news

xiangpin authored on 03/09/2020 02:04:32
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 + `geom_tiplab()` and `geom_nodelab()` support `geom = "shadowtext"`
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 + `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
6 6 
 + update man files of `geom_rootedge` and `geom_point2`
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++ update `geom_hilight` to support `geom_hilight(data = tbl_tree, node = selected_node)`. (2020-09-03, Thu)
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 # ggtree 2.3.4
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Browse code

defunct geom_nodelab2

Guangchuang Yu authored on 02/09/2020 09:28:48
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 # ggtree 2.3.4.992
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