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bump version

Guangchuang Yu authored on 06/11/2022 14:52:54
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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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+# ggtree 3.7.0.001
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+
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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
31 34
 
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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-# 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)
30 31
 + 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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   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
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+
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+# ggtree 3.5.3.001
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+
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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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   - <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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   - <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)
29 30
 + 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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linkage support

Guangchuang Yu authored on 11/08/2022 09:03:41
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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)
31
++ support 'linkage' class defined in the 'mdendro' package (2022-08-11, Thu)
30 32
 + clone the plot environment before assigning layout (2022-07-19, Tue, #516)
31 33
 + bug fixed in 'equal_angle' layout (2022-07-08, Fri, #514)
32 34
 + 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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-# ggtree 3.5.1.901
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+# ggtree 3.5.1.902
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++ clone the plot environment before assigning layout (2022-07-19, Tue, #516)
30 31
 + 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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update

Guangchuang Yu authored on 09/07/2022 07:33:16
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-# ggtree 3.5.1.900
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+# ggtree 3.5.1.901
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++ bug fixed in 'equal_angle' layout (2022-07-08, Fri, #514)
30 31
 + 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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+# 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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30 34
 + `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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-# ggtree 3.5.0.902
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++ `as.phylo.hclust2` to correct edge length as displayed in `stats:::plot.hclust` (2022-06-21, Tue)
30 31
 + add outline to nodepies (2022-06-20, Mon, #506)
31
-+ `update_edge_hclust()` to adjust edge length of a `phylo` object converted from a `hclust` object via `ape::as.phylo()` (2022-06-05, Sun)
32 32
 + new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497)
33 33
     - only works for Cartesian coordination, that means it will not work for `layout = 'radial'`
34 34
 
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update

Guangchuang Yu authored on 20/06/2022 07:13:19
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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)
30 31
 + `update_edge_hclust()` to adjust edge length of a `phylo` object converted from a `hclust` object via `ape::as.phylo()` (2022-06-05, Sun)
31 32
 + new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497)
32 33
     - only works for Cartesian coordination, that means it will not work for `layout = 'radial'`
Browse code

update_edge_hclust

Guangchuang Yu authored on 04/06/2022 17:02:02
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-# ggtree 3.5.0.900
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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)
30 31
 + new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497)
31 32
     - only works for Cartesian coordination, that means it will not work for `layout = 'radial'`
32 33
 
Browse code

update docs, #496, #497

Guangchuang Yu authored on 29/04/2022 08:02:38
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+# ggtree 3.5.0.900
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+
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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'`
32
+
33
+# ggtree 3.4.0
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+
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++ Bioconductor 3.15 release (2022-04-28, Thu)
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+
28 37
 # ggtree 3.3.3
29 38
 
30 39
 + `geom_striplab()` that supports `aes()` mapping (2022-04-22, Fri, #493)
Browse code

bump version

Guangchuang Yu authored on 24/04/2022 02:10:02
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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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++ `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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+
28 33
 # ggtree 3.3.2
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30 35
 + mv `identify()` method to 'ggfun' (2022-04-01, Fri)
Browse code

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()` 
Browse code

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()` 
31 32
 + update man files (2022-03-23, Wed, #489)
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 # ggtree 3.3.1
Browse code

update identify() method

Guangchuang Yu authored on 01/04/2022 02:45:58
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-# ggtree 3.3.1.900
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++ update `identify.gg()` to support 'ggplot' object and `+xlim()` (2022-04-01, Fri)
30 31
 + update man files (2022-03-23, Wed, #489)
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 # ggtree 3.3.1
Browse code

update man files and fixed R check

Guangchuang Yu authored on 23/03/2022 04:13:34
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   - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo> 
21 21
 + `fortify` method for `phyloseq` object should return a tidy data.frame
22 22
   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`
23
-+ update ggtree man files
24 23
 + The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
25 24
   - <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
30 33
   
31 34
 + use graph layouts to visualize tree (2021-12-10, Fri, #460, #461)
Browse code

bump version

Guangchuang Yu authored on 10/12/2021 09:53:25
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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 
8
-    + graphlayouts: <https://cran.r-project.org/web/packages/graphlayouts/index.html>
9
-    + TreeAndLeaf layout: <https://www.bioconductor.org/packages/TreeAndLeaf>
5
+
6
++ TreeAndLeaf layout: <https://www.bioconductor.org/packages/TreeAndLeaf>
10 7
 + `phylogeography`
11 8
   - <https://stackoverflow.com/questions/68668788/phylogeography-how-to-combine-phylogenetic-tree-and-geographic-map-and-create>
12 9
 + `phylomorphospace`
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-# ggtree 3.3.0.901
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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 
33
+  - graphlayouts: <https://cran.r-project.org/web/packages/graphlayouts/index.html>
34 34
 + `scale_color_subtree` and `scale_colour_subtree` to color subtree via taxa group information (e.g., cutree, or kmeans) (2021-12-01, Wed)
35 35
 + 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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 # 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>
9
+    + TreeAndLeaf layout: <https://www.bioconductor.org/packages/TreeAndLeaf>
5 10
 + `phylogeography`
6 11
   - <https://stackoverflow.com/questions/68668788/phylogeography-how-to-combine-phylogenetic-tree-and-geographic-map-and-create>
7 12
 + `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)
29
++ `scale_color_subtree` and `scale_colour_subtree` to color subtree via taxa group information (e.g., cutree, or kmeans) (2021-12-01, Wed)
30 30
 + set `na.value = 'white'` in `msaplot()` (2021-10-29, Fri)
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 # ggtree 3.2.0
Browse code

scale_color_subtree

Guangchuang Yu authored on 01/12/2021 08:14:20
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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)
29 30
 + set `na.value = 'white'` in `msaplot()` (2021-10-29, Fri)
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 # ggtree 3.2.0
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>
5 7
 + `phylomorphospace`
6 8
   - <https://github.com/YuLab-SMU/ggtree/issues/370>
7 9
   - <https://github.com/wabarr/ggphylomorpho>
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>
8
++ visualize support values obtained from different methods
9
+  - <https://github.com/YuLab-SMU/ggtree/issues/451>
8 10
 + `height` parameter to `collapse()`
9 11
   - <https://github.com/YuLab-SMU/ggtree/issues/409#issuecomment-944034311>
10 12
 + 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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 + `type` parameter in `geom_hilight` accepts 'roundrect' and 'gradient'
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   - <https://github.com/YuLab-SMU/ggtree/pull/444#issuecomment-949335277>
7 8
 + `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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+# 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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+  - <https://github.com/YuLab-SMU/ggtree/pull/444#issuecomment-949335277>
5 7
 + `height` parameter to `collapse()`
6 8
   - <https://github.com/YuLab-SMU/ggtree/issues/409#issuecomment-944034311>
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 + rewrite `revts` to `scale_revts`
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 # ggtree 3.1.6
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 + `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)
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 # 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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-# ggtree 3.1.5.902
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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`
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++ `inset` and relative functions support circular layout
7 9
 + tanglegram support
8 10
   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
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   - <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/>
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-+ `inset` and relative functions support circular layout
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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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++ `height` parameter to `collapse()`
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+  - <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> 
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update news

Guangchuang Yu authored on 14/10/2021 01:59:58
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+<!--
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+
1 3
 # TODO LIST
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3 5
 + tanglegram support
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 + `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/>
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++ `inset` and relative functions support circular layout
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+
19
+-->
15 20
 
16 21
 
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-# ggtree 3.1.5.901
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+# ggtree 3.1.5.902
18 23
 
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++ `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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   - <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
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+# 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
 
Guangchuang Yu authored on 05/10/2021 06:16:49
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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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   - <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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 + rewrite `revts` to `scale_revts`
12 12
 
13 13
 
14
-# ggtree 3.1.4.993
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+# ggtree 3.1.5
15 15
 
16
-+ `ggdensitree` with `align.tips=TRUE` sets max x to 0 (2021-09-26, Sun, @brj1, #439)
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++ `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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-# ggtree 3.1.4.992
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+# 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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-# ggtree 3.1.4.991
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+# 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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+# 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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-# ggtree 3.1.3.993
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+# 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
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+# 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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-# ggtree 3.1.3.991
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+# 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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-# 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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+# 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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-# 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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+# 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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-# 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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+# 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
Showing1 changed files
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-# ggtree 2.5.0.992
1
+# ggtree 2.5.0.993
2 2
 
3
++ `label` and `offset.label` introduced in `geom_treescale` layer (2020-12-23, Wed)
4
+  - <https://github.com/YuLab-SMU/ggtree/pull/360>
5
++ `geom_rootedge` supports reversed x (2020-12-17, Thu)
6
+  - <https://github.com/YuLab-SMU/ggtree/pull/358>
3 7
 + `geom_nodelab()` now supports circular layout (2020-11-26, Thu)
4 8
   - <https://github.com/YuLab-SMU/ggtree/issues/352>
5 9
   - <https://github.com/YuLab-SMU/ggtree/pull/353>
Browse code

update docs

Guangchuang Yu authored on 26/11/2020 06:52:14
Showing1 changed files
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1
-# ggtree 2.5.0.991
1
+# ggtree 2.5.0.992
2 2
 
3
++ `geom_nodelab()` now supports circular layout (2020-11-26, Thu)
4
+  - <https://github.com/YuLab-SMU/ggtree/issues/352>
5
+  - <https://github.com/YuLab-SMU/ggtree/pull/353>
3 6
 + branch size can be grandualy changed (2020-10-29, Thu)
4 7
   - <https://github.com/YuLab-SMU/ggtree/pull/349>
5 8
 
Browse code

update url

Guangchuang Yu authored on 13/11/2020 14:29:27
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@@ -2,7 +2,7 @@
2 2
 
3 3
 + branch size can be grandualy changed (2020-10-29, Thu)
4 4
   - <https://github.com/YuLab-SMU/ggtree/pull/349>
5
-  
5
+
6 6
 # ggtree 2.4.0
7 7
 
8 8
 + Bioconductor 3.12 release (2020-10-28, Wed)
Browse code

bump version

Guangchuang Yu authored on 29/10/2020 00:40:31
Showing1 changed files
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1
+# ggtree 2.5.0.991
2
+
3
++ branch size can be grandualy changed (2020-10-29, Thu)
4
+  - <https://github.com/YuLab-SMU/ggtree/pull/349>
5
+  
1 6
 # ggtree 2.4.0
2 7
 
3 8
 + Bioconductor 3.12 release (2020-10-28, Wed)
Browse code

new release

Guangchuang Yu authored on 28/10/2020 00:32:17
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1
+# ggtree 2.4.0
2
+
3
++ Bioconductor 3.12 release (2020-10-28, Wed)
4
+
1 5
 # ggtree 2.3.7
2 6
 
3 7
 + 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
1
+# ggtree 2.3.7
2 2
 
3 3
 + add `label_pad()` function to add padding characters to taxa labels (2020-10-09, Fri)
4 4
   - <https://groups.google.com/g/bioc-ggtree/c/INJ0Nfkq3b0/m/lXefnfV5AQAJ>
Browse code

label_pad

Guangchuang Yu authored on 09/10/2020 15:27:38
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+# ggtree 2.3.6.991
2
+
3
++ add `label_pad()` function to add padding characters to taxa labels (2020-10-09, Fri)
4
+  - <https://groups.google.com/g/bioc-ggtree/c/INJ0Nfkq3b0/m/lXefnfV5AQAJ>
5
++ add `family` parameter to `geom_tiplab()` 
6
+
1 7
 # ggtree 2.3.6
2 8
 
3 9
 + new layouts, `roundrect` and `ellipse`
Browse code

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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+# ggtree 2.3.6
2 2
 
3
++ new layouts, `roundrect` and `ellipse`
4
+  - <https://github.com/YuLab-SMU/ggtree/pull/344>
5
+  - <https://github.com/YuLab-SMU/ggtree/pull/346>
3 6
 + `fortify()` method for `treedataList` object (2020-09-20, Sun)
4 7
 + `vexpand()` and `ggexpand()` to expand plot limit by ratio of plot range (2020-09-18, Fri) 
5 8
 + `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
1
+# ggtree 2.3.5.993
2 2
 
3
++ `fortify()` method for `treedataList` object (2020-09-20, Sun)
3 4
 + `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
2 2
 
3
-+ `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>
5 6
 
6 7
 # ggtree 2.3.5
Browse code

update docs

Guangchuang Yu authored on 17/09/2020 01:45:18
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@@ -1,3 +1,8 @@
1
+# ggtree 2.3.5.991
2
+
3
++ `geom_cladelab`, an updated version of `geom_cladelabel` that supports aes mapping (2020-09-17, Thu)
4
+  - <https://github.com/YuLab-SMU/ggtree/pull/342>
5
+
1 6
 # ggtree 2.3.5
2 7
 
3 8
 + `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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@@ -1,9 +1,12 @@
1
-# ggtree 2.3.4.993
1
+# ggtree 2.3.5
2 2
 
3
++ `td_unnest()` which return a function to flatten ggtree plot data (2020-09-14, Mon)
4
+  - <https://yulab-smu.top/treedata-book/chapter12.html#td_unnest>
3 5
 + update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)
4 6
 + Defunct `geom_nodelab2()` (2020-09-02, Wed)
5 7
 + `geom_tiplab()` and `geom_nodelab()` support `geom = "shadowtext"` 
6
-+ `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
8
++ `td_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
9
+  - <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)
9 12
 
Browse code

update docs

Guangchuang Yu authored on 03/09/2020 02:53:24
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@@ -1,5 +1,6 @@
1
-# ggtree 2.3.4.992
1
+# ggtree 2.3.4.993
2 2
 
3
++ 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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@@ -4,6 +4,7 @@
4 4
 + `geom_tiplab()` and `geom_nodelab()` support `geom = "shadowtext"` 
5 5
 + `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`
7
++ update `geom_hilight` to support `geom_hilight(data = tbl_tree, node = selected_node)`. (2020-09-03, Thu)
7 8
 
8 9
 # ggtree 2.3.4
9 10
 
Browse code

defunct geom_nodelab2

Guangchuang Yu authored on 02/09/2020 09:28:48
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@@ -1,6 +1,7 @@
1 1
 # ggtree 2.3.4.992
2 2
 
3
-+ `geom_tiplab()` support `geom = "shadowtext"` (2020-09-02, Wed)
3
++ Defunct `geom_nodelab2()` (2020-09-02, Wed)
4
++ `geom_tiplab()` and `geom_nodelab()` support `geom = "shadowtext"` 
4 5
 + `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
5 6
 + update man files of `geom_rootedge` and `geom_point2`
6 7
 
Browse code

shadowtext

Guangchuang Yu authored on 02/09/2020 08:44:40
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@@ -1,5 +1,6 @@
1
-# ggtree 2.3.4.991
1
+# ggtree 2.3.4.992
2 2
 
3
++ `geom_tiplab()` support `geom = "shadowtext"` (2020-09-02, Wed)
3 4
 + `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
4 5
 + update man files of `geom_rootedge` and `geom_point2`
5 6
 
Browse code

update man

Guangchuang Yu authored on 30/08/2020 09:34:25
Showing1 changed files
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@@ -1,6 +1,6 @@
1 1
 # ggtree 2.3.4.991
2 2
 
3
-+ `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sta)
3
++ `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
4 4
 + update man files of `geom_rootedge` and `geom_point2`
5 5
 
6 6
 # ggtree 2.3.4
Browse code

tree_filter

Guangchuang Yu authored on 29/08/2020 05:49:35
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@@ -1,3 +1,8 @@
1
+# ggtree 2.3.4.991
2
+
3
++ `tree_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sta)
4
++ update man files of `geom_rootedge` and `geom_point2`
5
+
1 6
 # ggtree 2.3.4
2 7
 
3 8
 + `zoomClade` and `geom_zoom_clade` to zoom in selected clade (2020-08-04, Tue)
Browse code

zoomClade and geom_zoom_clade

Guangchuang Yu authored on 03/08/2020 16:21:17
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@@ -1,5 +1,7 @@
1
-# ggtree 2.3.3.993
1
+# ggtree 2.3.4
2 2
 
3
++ `zoomClade` and `geom_zoom_clade` to zoom in selected clade (2020-08-04, Tue)
4
+  - these two functions are wrapper function of `ggforce::facet_zoom`
3 5
 + update `facet_labeller` according to the change of `ggplot2` (2020-07-28, Tue)
4 6
 + defunct `set_hilight_legend` as now `geom_hilight` supports aesthetic mapping and can generate legend automotically 
5 7
 + remove `annotation_image`, `phylopic` and `subview` as they were defunct for quite a long time. Users should refer to the `ggimage` package if they want to annotate tree with image or subplots.
Browse code

update

Guangchuang Yu authored on 28/07/2020 08:37:55
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@@ -1,6 +1,7 @@
1 1
 # ggtree 2.3.3.993
2 2
 
3
-+ defunct `set_hilight_legend` as now `geom_hilight` supports aesthetic mapping and can generate legend automotically (2020-07-28, Tue)
3
++ update `facet_labeller` according to the change of `ggplot2` (2020-07-28, Tue)
4
++ defunct `set_hilight_legend` as now `geom_hilight` supports aesthetic mapping and can generate legend automotically 
4 5
 + remove `annotation_image`, `phylopic` and `subview` as they were defunct for quite a long time. Users should refer to the `ggimage` package if they want to annotate tree with image or subplots.
5 6
 + `as_ylab` parameter added in `geom_tiplab()`, which supports displaying tip labels as y-axis label and only works for rectangular and dendrogram layouts 
6 7
 + `hexpand` to expand x limits by ratio of x range and supports both direction (1 for rhs and -1 for lhs) (2020-07-27, Mon)
Browse code

remove functions

Guangchuang Yu authored on 28/07/2020 07:02:57
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@@ -1,6 +1,8 @@
1
-# ggtree 2.3.3.992
1
+# ggtree 2.3.3.993
2 2
 
3
-+ `as_ylab` parameter added in `geom_tiplab()`, which supports displaying tip labels as y-axis label and only works for rectangular and dendrogram layouts (2020-07-28, Tue)
3
++ defunct `set_hilight_legend` as now `geom_hilight` supports aesthetic mapping and can generate legend automotically (2020-07-28, Tue)
4
++ remove `annotation_image`, `phylopic` and `subview` as they were defunct for quite a long time. Users should refer to the `ggimage` package if they want to annotate tree with image or subplots.
5
++ `as_ylab` parameter added in `geom_tiplab()`, which supports displaying tip labels as y-axis label and only works for rectangular and dendrogram layouts 
4 6
 + `hexpand` to expand x limits by ratio of x range and supports both direction (1 for rhs and -1 for lhs) (2020-07-27, Mon)
5 7
 
6 8
 # ggtree 2.3.3
Browse code

as_ylab in geom_tiplab()

Guangchuang Yu authored on 28/07/2020 06:36:51
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@@ -1,6 +1,6 @@
1 1
 # ggtree 2.3.3.992
2 2
 
3
-+ `as_ylab` parameter added in `geom_tiplab()`, which supports displaying tip labels as y-axis label and only works for rectangular layout (2020-07-28, Tue)
3
++ `as_ylab` parameter added in `geom_tiplab()`, which supports displaying tip labels as y-axis label and only works for rectangular and dendrogram layouts (2020-07-28, Tue)
4 4
 + `hexpand` to expand x limits by ratio of x range and supports both direction (1 for rhs and -1 for lhs) (2020-07-27, Mon)
5 5
 
6 6
 # ggtree 2.3.3
Browse code

as_ylab in geom_tiplab()

Guangchuang Yu authored on 28/07/2020 06:04:40
Showing1 changed files
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@@ -1,5 +1,6 @@
1
-# ggtree 2.3.3.991
1
+# ggtree 2.3.3.992
2 2
 
3
++ `as_ylab` parameter added in `geom_tiplab()`, which supports displaying tip labels as y-axis label and only works for rectangular layout (2020-07-28, Tue)
3 4
 + `hexpand` to expand x limits by ratio of x range and supports both direction (1 for rhs and -1 for lhs) (2020-07-27, Mon)
4 5
 
5 6
 # ggtree 2.3.3
Browse code

hexpand

Guangchuang Yu authored on 27/07/2020 11:40:01
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@@ -1,3 +1,7 @@
1
+# ggtree 2.3.3.991
2
+
3
++ `hexpand` to expand x limits by ratio of x range and supports both direction (1 for rhs and -1 for lhs) (2020-07-27, Mon)
4
+
1 5
 # ggtree 2.3.3
2 6
 
3 7
 + add `type` parameter in `geom_hilight`, default is `auto`, optional `rect` 
Browse code

bump version up and commit to bioconductor

Guangchuang Yu authored on 23/07/2020 07:31:36
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@@ -1,4 +1,4 @@
1
-# ggtree 2.3.2.993
1
+# ggtree 2.3.3
2 2
 
3 3
 + add `type` parameter in `geom_hilight`, default is `auto`, optional `rect` 
4 4
   to `rectangular` layer, `encircle` to `encircle` layer and comment original 
Browse code

update doc

xiangpin authored on 23/07/2020 06:31:17
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@@ -1,5 +1,8 @@
1 1
 # ggtree 2.3.2.993
2 2
 
3
++ add `type` parameter in `geom_hilight`, default is `auto`, optional `rect` 
4
+  to `rectangular` layer, `encircle` to `encircle` layer and comment original 
5
+  `geom_hilight`, and support `subset` in aesthetic. (2020-07-23, Thu)
3 6
 + update `geom_hilight` to support aesthetic mapping (2020-07-22, Wed)
4 7
 + update `geom_taxalink` to support aesthetic mapping (2020-07-20, Mon)
5 8
 + `layout_inward_circular` for `layout_circular() + scale_x_reverse()` (2020-07-16, Thu)
Browse code

update docs

Guangchuang Yu authored on 22/07/2020 09:34:15
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@@ -1,6 +1,6 @@
1
-# ggtree 2.3.2.992
1
+# ggtree 2.3.2.993
2 2
 
3
-+ add `geom_hilight2` to support aesthetic mapping (2020-07-22, Wed)
3
++ update `geom_hilight` to support aesthetic mapping (2020-07-22, Wed)
4 4
 + update `geom_taxalink` to support aesthetic mapping (2020-07-20, Mon)
5 5
 + `layout_inward_circular` for `layout_circular() + scale_x_reverse()` (2020-07-16, Thu)
6 6
 
Browse code

update doc

xiangpin authored on 22/07/2020 06:23:28
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@@ -1,5 +1,6 @@
1 1
 # ggtree 2.3.2.992
2 2
 
3
++ add `geom_hilight2` to support aesthetic mapping (2020-07-22, Wed)
3 4
 + update `geom_taxalink` to support aesthetic mapping (2020-07-20, Mon)
4 5
 + `layout_inward_circular` for `layout_circular() + scale_x_reverse()` (2020-07-16, Thu)
5 6
 
Browse code

geom_taxalink supports aes mapping

Guangchuang Yu authored on 20/07/2020 14:59:17
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@@ -1,5 +1,6 @@
1
-# ggtree 2.3.2.991
1
+# ggtree 2.3.2.992
2 2
 
3
++ update `geom_taxalink` to support aesthetic mapping (2020-07-20, Mon)
3 4
 + `layout_inward_circular` for `layout_circular() + scale_x_reverse()` (2020-07-16, Thu)
4 5
 
5 6
 # ggtree 2.3.2
Browse code

layout_inward_circular

Guangchuang Yu authored on 16/07/2020 10:30:54
Showing1 changed files
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@@ -1,3 +1,7 @@
1
+# ggtree 2.3.2.991
2
+
3
++ `layout_inward_circular` for `layout_circular() + scale_x_reverse()` (2020-07-16, Thu)
4
+
1 5
 # ggtree 2.3.2
2 6
 
3 7
 + update `geom_taxalink` to support circular layout tree (2020-07-13, Mon).
Browse code

update version and docs

xiangpin authored on 13/07/2020 03:05:20
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@@ -1,3 +1,7 @@
1
+# ggtree 2.3.2
2
+
3
++ update `geom_taxalink` to support circular layout tree (2020-07-13, Mon).
4
+
1 5
 # ggtree 2.3.1
2 6
 
3 7
 + `fortify` method for `pvclust` object (2020-06-21, Mon)
Browse code

fortify method for pvclust

Guangchuang Yu authored on 22/06/2020 02:48:45
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@@ -1,5 +1,6 @@
1
-# ggtree 2.3.0.992
1
+# ggtree 2.3.1
2 2
 
3
++ `fortify` method for `pvclust` object (2020-06-21, Mon)
3 4
 + add dot parameters for color or size of `geom_hilight` and more detail messages of
4 5
   warnings for `extendto`. (2020-06-16, Tue)
5 6
 + modified the angle of clade labels. Added horizontal parameter to control
Browse code

update doc

xiangpin authored on 16/06/2020 12:57:07
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... ...
@@ -1,5 +1,7 @@
1 1
 # ggtree 2.3.0.992
2 2
 
3
++ add dot parameters for color or size of `geom_hilight` and more detail messages of
4
+  warnings for `extendto`. (2020-06-16, Tue)
3 5
 + modified the angle of clade labels. Added horizontal parameter to control
4 6
   whether set clade labels to horizontal. When the parameter was set to `FALSE`, 
5 7
   it will be useful for the layouts in `coord_polar`, such as `circular`, `fan`,
Browse code

update docs

Guangchuang Yu authored on 15/06/2020 07:37:01
Showing1 changed files
... ...
@@ -3,10 +3,7 @@
3 3
 + modified the angle of clade labels. Added horizontal parameter to control
4 4
   whether set clade labels to horizontal. When the parameter was set to `FALSE`, 
5 5
   it will be useful for the layouts in `coord_polar`, such as `circular`, `fan`,
6
-  `radial`. To better view the clade labels, their angles has been adjusted.
7
-
8
-# ggtree 2.3.0.991
9
-
6
+  `radial`. To better view the clade labels, their angles has been adjusted. (2020-06-15, Mon)
10 7
 + bug fixed in `getYcoord_scale_category` (2020-05-13, Wed)
11 8
 
12 9
 # ggtree 2.2.0
Browse code

add version and update log of version

xiangpin authored on 15/06/2020 05:03:37
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@@ -1,3 +1,10 @@
1
+# ggtree 2.3.0.992
2
+
3
++ modified the angle of clade labels. Added horizontal parameter to control
4
+  whether set clade labels to horizontal. When the parameter was set to `FALSE`, 
5
+  it will be useful for the layouts in `coord_polar`, such as `circular`, `fan`,
6
+  `radial`. To better view the clade labels, their angles has been adjusted.
7
+
1 8
 # ggtree 2.3.0.991
2 9
 
3 10
 + bug fixed in `getYcoord_scale_category` (2020-05-13, Wed)
Browse code

bug fixed

Guangchuang Yu authored on 13/05/2020 10:20:21
Showing1 changed files
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@@ -1,3 +1,11 @@
1
+# ggtree 2.3.0.991
2
+
3
++ bug fixed in `getYcoord_scale_category` (2020-05-13, Wed)
4
+
5
+# ggtree 2.2.0
6
+
7
++ Bioconductor 3.11 release
8
+
1 9
 # ggtree 2.1.6
2 10
 
3 11
 + Now `geom_tiplab()` works with unrooted layouts (`ape`, `equal_angle` and `daylight`) (2020-04-23, Thu)
Browse code

geom_tiplab() works with unrooted layout, #292

Guangchuang Yu authored on 23/04/2020 03:13:24
Showing1 changed files
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@@ -1,5 +1,7 @@
1 1
 # ggtree 2.1.6
2 2
 
3
++ Now `geom_tiplab()` works with unrooted layouts (`ape`, `equal_angle` and `daylight`) (2020-04-23, Thu)
4
+  - <https://github.com/YuLab-SMU/ggtree/issues/292>
3 5
 + bug fixed of `layoutEqualAngle` (2020-04-09, Thu)
4 6
   - in tibble v=3.0.0, df$x = NA will store df$x as lgl variable and assign numeric value to df$x will throw error. Now change to df$x = 0 in `layoutEqualAngle`. 
5 7
 
Browse code

bump version

Guangchuang Yu authored on 09/04/2020 02:08:39
Showing1 changed files
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@@ -1,8 +1,11 @@
1
-# ggtree 2.1.5
1
+# ggtree 2.1.6
2 2
 
3 3
 + bug fixed of `layoutEqualAngle` (2020-04-09, Thu)
4 4
   - in tibble v=3.0.0, df$x = NA will store df$x as lgl variable and assign numeric value to df$x will throw error. Now change to df$x = 0 in `layoutEqualAngle`. 
5
-+ bug fixed of calculating inset width and height 
5
+
6
+# ggtree 2.1.5
7
+
8
++ bug fixed of calculating inset width and height
6 9
   - <https://github.com/YuLab-SMU/ggtree/issues/289>
7 10
 
8 11
 # ggtree 2.1.4
Browse code

bug fixed of layoutEqualAngle

Guangchuang Yu authored on 09/04/2020 02:07:12
Showing1 changed files
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@@ -1,8 +1,10 @@
1 1
 # ggtree 2.1.5
2 2
 
3
-+ bug fixed of calculating inset width and height (2020-04-09, Thu)
3
++ bug fixed of `layoutEqualAngle` (2020-04-09, Thu)
4
+  - in tibble v=3.0.0, df$x = NA will store df$x as lgl variable and assign numeric value to df$x will throw error. Now change to df$x = 0 in `layoutEqualAngle`. 
5
++ bug fixed of calculating inset width and height 
4 6
   - <https://github.com/YuLab-SMU/ggtree/issues/289>
5
-  
7
+
6 8
 # ggtree 2.1.4
7 9
 
8 10
 + import `aplot::xrange` 
Browse code

bug fixed of calculating inset width and height, #289

Guangchuang Yu authored on 09/04/2020 01:11:31
Showing1 changed files
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@@ -1,3 +1,12 @@
1
+# ggtree 2.1.5
2
+
3
++ bug fixed of calculating inset width and height (2020-04-09, Thu)
4
+  - <https://github.com/YuLab-SMU/ggtree/issues/289>
5
+  
6
+# ggtree 2.1.4
7
+
8
++ import `aplot::xrange` 
9
+
1 10
 # ggtree 2.1.3
2 11
 
3 12
 + move `xlim2` and `ylim2` to aplot package (2020-03-30, Mon)
Guangchuang Yu authored on 31/03/2020 04:16:05
Showing1 changed files
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@@ -1,5 +1,7 @@
1 1
 # ggtree 2.1.3
2 2
 
3
++ move `xlim2` and `ylim2` to aplot package (2020-03-30, Mon)
4
+  - <https://cran.r-project.org/package=aplot>
3 5
 + remove `mutate_` as it was deprecated in dplyr (2020-03-25, Wed)
4 6
 + fixed mutate bug caused by new version of dplyr and tidytree in daylight layout (2020-03-16, Mon)
5 7
   - <https://github.com/YuLab-SMU/ggtree/issues/282>
Browse code

remove mutate_

Guangchuang Yu authored on 25/03/2020 03:58:15
Showing1 changed files
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@@ -1,8 +1,9 @@
1 1
 # ggtree 2.1.3
2 2
 
3
++ remove `mutate_` as it was deprecated in dplyr (2020-03-25, Wed)
3 4
 + fixed mutate bug caused by new version of dplyr and tidytree in daylight layout (2020-03-16, Mon)
4 5
   - <https://github.com/YuLab-SMU/ggtree/issues/282>
5
-  
6
+
6 7
 # ggtree 2.1.2
7 8
 
8 9
 + `expand_scale` was deprecated in ggplot2 v=3.3.0, import `expansion` instead (2020-03-12, Thu)
Browse code

bug fixed, #282

Guangchuang Yu authored on 16/03/2020 06:27:18
Showing1 changed files
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@@ -1,3 +1,8 @@
1
+# ggtree 2.1.3
2
+
3
++ fixed mutate bug caused by new version of dplyr and tidytree in daylight layout (2020-03-16, Mon)
4
+  - <https://github.com/YuLab-SMU/ggtree/issues/282>
5
+  
1 6
 # ggtree 2.1.2
2 7
 
3 8
 + `expand_scale` was deprecated in ggplot2 v=3.3.0, import `expansion` instead (2020-03-12, Thu)
Browse code

import expansion

Guangchuang Yu authored on 12/03/2020 09:27:40
Showing1 changed files
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@@ -1,5 +1,6 @@
1 1
 # ggtree 2.1.2
2 2
 
3
++ `expand_scale` was deprecated in ggplot2 v=3.3.0, import `expansion` instead (2020-03-12, Thu)
3 4
 + bug fixed of determined layout for `ggplot(tree) + geom_tiplab()` (2020-01-26, Sun)
4 5
   - <https://github.com/YuLab-SMU/ggtree/issues/272>
5 6
 + set unrooted layout to use `coord_fixed` by default (2020-01-25, Sat)
Browse code

fixing incorrect links

brj1 authored on 27/01/2020 22:49:39
Showing1 changed files
... ...
@@ -4,7 +4,7 @@
4 4
   - <https://github.com/YuLab-SMU/ggtree/issues/272>
5 5
 + set unrooted layout to use `coord_fixed` by default (2020-01-25, Sat)
6 6
 + if `layout = "ape"`, use ape unrooted layout 
7
-  - <https://github.com/YuLab-SMU/ggtree/issues/272>
7
+  - <https://github.com/YuLab-SMU/ggtree/pull/273>
8 8
 
9 9
 # ggtree 2.1.1
10 10
 
Browse code

bug fixed

Guangchuang Yu authored on 26/01/2020 15:25:32
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1
+# ggtree 2.1.2
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+
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++ bug fixed of determined layout for `ggplot(tree) + geom_tiplab()` (2020-01-26, Sun)
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+  - <https://github.com/YuLab-SMU/ggtree/issues/272>
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++ set unrooted layout to use `coord_fixed` by default (2020-01-25, Sat)
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++ if `layout = "ape"`, use ape unrooted layout 
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+  - <https://github.com/YuLab-SMU/ggtree/issues/272>
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+
1 9
 # ggtree 2.1.1
2 10
 
3 11
 + export `geom_highlight` as an alias of `geom_hilight` (2020-01-08, Wed)
Browse code

geom_highlight

Guangchuang Yu authored on 08/01/2020 02:55:39
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1 1
 # ggtree 2.1.1
2 2
 
3
++ export `geom_highlight` as an alias of `geom_hilight` (2020-01-08, Wed)
3 4
 + set `clip="off"` for all layouts (2019-12-06, Fri)
4 5
 + not passing `fontface` if `geom` is `image` or `phylopic` in `geom_tiplab` and `geom_nodelab` (2019-11-29, Fri)
5 6
 + import and re-export `guide_legend`, `scale_colour_manual`, `scale_color_manual`, `scale_fill_manual` and `margin` from `ggplot2`
Browse code

clip="off" and update docs

Guangchuang Yu authored on 06/12/2019 03:01:17
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1 1
 # ggtree 2.1.1
2 2
 
3
++ set `clip="off"` for all layouts (2019-12-06, Fri)
3 4
 + not passing `fontface` if `geom` is `image` or `phylopic` in `geom_tiplab` and `geom_nodelab` (2019-11-29, Fri)
4 5
 + import and re-export `guide_legend`, `scale_colour_manual`, `scale_color_manual`, `scale_fill_manual` and `margin` from `ggplot2`
5 6
 + `offspring` method for `ggtree` object (2019-11-21, Thu)
Browse code

fixed warnings

Guangchuang Yu authored on 29/11/2019 07:47:41
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1 1
 # ggtree 2.1.1
2 2
 
3
++ not passing `fontface` if `geom` is `image` or `phylopic` in `geom_tiplab` and `geom_nodelab` (2019-11-29, Fri)
4
++ import and re-export `guide_legend`, `scale_colour_manual`, `scale_color_manual`, `scale_fill_manual` and `margin` from `ggplot2`
3 5
 + `offspring` method for `ggtree` object (2019-11-21, Thu)
4 6
 + fixed `revts` to work with `collapse` (2019-11-18, Mon)
5 7
 + convert roxygen documents using markdown (2019-11-01, Fri)
Browse code

offspring method for ggtree object

Guangchuang Yu authored on 21/11/2019 08:13:29
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1 1
 # ggtree 2.1.1
2 2
 
3
++ `offspring` method for `ggtree` object (2019-11-21, Thu)
3 4
 + fixed `revts` to work with `collapse` (2019-11-18, Mon)
4 5
 + convert roxygen documents using markdown (2019-11-01, Fri)
5 6
 + extend `xlim2` and `ylim2` to support discrete scale.
Browse code

bug fixed

Guangchuang Yu authored on 18/11/2019 12:16:56
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1 1
 # ggtree 2.1.1
2 2
 
3
++ fixed `revts` to work with `collapse` (2019-11-18, Mon)
3 4
 + convert roxygen documents using markdown (2019-11-01, Fri)
4 5
 + extend `xlim2` and `ylim2` to support discrete scale.
5 6
 + `xlim2` and `ylim2` to uniformize axis limits of ggplot objects (2019-10-31, Thu)
Browse code

extend `xlim2` and `ylim2` to support discrete scale.

Guangchuang Yu authored on 01/11/2019 09:06:55
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1 1
 # ggtree 2.1.1
2 2
 
3 3
 + convert roxygen documents using markdown (2019-11-01, Fri)
4
++ extend `xlim2` and `ylim2` to support discrete scale.
4 5
 + `xlim2` and `ylim2` to uniformize axis limits of ggplot objects (2019-10-31, Thu)
5 6
   - <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot>
6 7
   - <https://yulab-smu.github.io/treedata-book/docs/chapter10.html#axis_align>
Browse code

xlim2 and ylim2

Guangchuang Yu authored on 01/11/2019 05:57:59
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1 1
 # ggtree 2.1.1
2 2
 
3 3
 + convert roxygen documents using markdown (2019-11-01, Fri)
4
-+ `xlim_align` and `ylim_align` to uniformize axis limits of ggplot objects (2019-10-31, Thu)
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++ `xlim2` and `ylim2` to uniformize axis limits of ggplot objects (2019-10-31, Thu)
5 5
   - <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot>
6 6
   - <https://yulab-smu.github.io/treedata-book/docs/chapter10.html#axis_align>
7 7
 + fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed)
Browse code

roxygen2md

Guangchuang Yu authored on 01/11/2019 04:24:00
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 # ggtree 2.1.1
2 2
 
3
-+ `align_x` and `align_y` for setting x or y limits of a ggplot based on another ggplot object (2019-10-31, Thu)
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++ convert roxygen documents using markdown (2019-11-01, Fri)
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++ `xlim_align` and `ylim_align` to uniformize axis limits of ggplot objects (2019-10-31, Thu)
4 5
   - <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot>
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+  - <https://yulab-smu.github.io/treedata-book/docs/chapter10.html#axis_align>
5 7
 + fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed)
6 8
   - <https://github.com/YuLab-SMU/ggtree/issues/260>
7 9
 
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align_x and align_y

Guangchuang Yu authored on 31/10/2019 09:28:27
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 # ggtree 2.1.1
2 2
 
3
-+ `ylim_ggtree` for setting y limits of a ggplot based on y limits of input ggtree object (2019-10-31, Thu)
3
++ `align_x` and `align_y` for setting x or y limits of a ggplot based on another ggplot object (2019-10-31, Thu)
4 4
   - <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot>
5 5
 + fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed)
6 6
   - <https://github.com/YuLab-SMU/ggtree/issues/260>
Browse code

ylim_ggtree

Guangchuang Yu authored on 31/10/2019 07:16:49
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 # ggtree 2.1.1
2 2
 
3
++ `ylim_ggtree` for setting y limits of a ggplot based on y limits of input ggtree object (2019-10-31, Thu)
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+  - <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot>
3 5
 + fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed)
4 6
   - <https://github.com/YuLab-SMU/ggtree/issues/260>
5 7
 
Browse code

fixed warning

Guangchuang Yu authored on 30/10/2019 02:03:01
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+# ggtree 2.1.1
2
+
3
++ fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed)
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+  - <https://github.com/YuLab-SMU/ggtree/issues/260>
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+
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+# ggtree 2.0.0
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+
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++ Bioconductor 3.10 release (2019-10-30, Wed)
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+
1 10
 # ggtree 1.99.1
2 11
 
3 12
 + bug fixed of `geom_hilight` for `tree$edge.length = NULL` (2019-10-16, Wed)
Browse code

bug fixed of geom_hilight

Guangchuang Yu authored on 16/10/2019 07:58:39
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1 1
 # ggtree 1.99.1
2 2
 
3
++ bug fixed of `geom_hilight` for `tree$edge.length = NULL` (2019-10-16, Wed)
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+  - <https://groups.google.com/d/msg/bioc-ggtree/GULj-eoAluI/Llpm-HbfCwAJ>
3 5
 + `fortify` method for igraph (only work with tree graph) (2019-09-28, Sat)
4 6
 + `ggdensitree` (2019-09-11, Wed)
5 7
   - <https://github.com/YuLab-SMU/ggtree/pull/253>
Browse code

fortify for tree graph

Guangchuang Yu authored on 28/09/2019 09:25:27
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 # ggtree 1.99.1
2 2
 
3
++ `fortify` method for igraph (only work with tree graph) (2019-09-28, Sat)
3 4
 + `ggdensitree` (2019-09-11, Wed)
4 5
   - <https://github.com/YuLab-SMU/ggtree/pull/253>
5 6
   - <https://github.com/YuLab-SMU/ggtree/pull/255> 
Browse code

update docs

Guangchuang Yu authored on 12/09/2019 01:15:16
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2 2
 
3 3
 + `ggdensitree` (2019-09-11, Wed)
4 4
   - <https://github.com/YuLab-SMU/ggtree/pull/253>
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-  
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+  - <https://github.com/YuLab-SMU/ggtree/pull/255> 
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+  - <https://yulab-smu.github.io/treedata-book/chapter4.html#visualize-a-list-of-trees>
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+
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 # ggtree 1.99.0
7 9
 
8 10
 + prepare for ggtree v=2.0.0
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11 13
 
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 + `fortify` methods for hierarchical clustering objects, including `agnes`, `diana` and `twins` (2019-08-30, Fri) 
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 + now `geom_hilight` supports `unrooted` and `daylight` layouts (2019-08-28, Wed)
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+  - by calling `geom_hilight_encircle`
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 + update `geom_motif` according to the change of `gggenes` and allow labeling genes (2019-08-27, Tue)
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   - <https://yulab-smu.github.io/treedata-book/chapter11.html#genome-locus>
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 + re-implement `geom_strip` with more robust support of labelling strip, either input taxa using name or id.
Browse code

ggdensitree

Guangchuang Yu authored on 11/09/2019 01:39:19
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+# ggtree 1.99.1
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+
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++ `ggdensitree` (2019-09-11, Wed)
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+  - <https://github.com/YuLab-SMU/ggtree/pull/253>
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+  
1 6
 # ggtree 1.99.0
2 7
 
3 8
 + prepare for ggtree v=2.0.0
Browse code

1.99.0

Guangchuang Yu authored on 02/09/2019 07:19:41
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