... | ... |
@@ -26,8 +26,9 @@ |
26 | 26 |
|
27 | 27 |
--> |
28 | 28 |
|
29 |
-# ggtree 3.7.0.001 |
|
29 |
+# ggtree 3.7.1 |
|
30 | 30 |
|
31 |
++ compatible with ggplot2 v=3.4.0 (2022-11-07, Mon) |
|
31 | 32 |
+ 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) |
32 | 33 |
|
33 | 34 |
# ggtree 3.6.0 |
... | ... |
@@ -26,6 +26,9 @@ |
26 | 26 |
|
27 | 27 |
--> |
28 | 28 |
|
29 |
+# ggtree 3.7.0.001 |
|
30 |
+ |
|
31 |
++ 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) |
|
29 | 32 |
|
30 | 33 |
# ggtree 3.6.0 |
31 | 34 |
|
... | ... |
@@ -24,6 +24,11 @@ |
24 | 24 |
- <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211> |
25 | 25 |
|
26 | 26 |
--> |
27 |
+ |
|
28 |
+# ggtree 3.5.3.001 |
|
29 |
+ |
|
30 |
++ move `scale_color_subtree()` to the 'ggtreeDendro' package (2022-09-23, Fri) |
|
31 |
+ |
|
27 | 32 |
# ggtree 3.5.3 |
28 | 33 |
|
29 | 34 |
+ update `fortify` method for `pvclust` object (2022-08-15, Mon) |
... | ... |
@@ -24,7 +24,7 @@ |
24 | 24 |
- <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211> |
25 | 25 |
|
26 | 26 |
--> |
27 |
-# ggtree 3.5.2.992 |
|
27 |
+# ggtree 3.5.3 |
|
28 | 28 |
|
29 | 29 |
+ update `fortify` method for `pvclust` object (2022-08-15, Mon) |
30 | 30 |
+ add citation of the tree data book (2022-08-13, Sat) |
... | ... |
@@ -24,8 +24,9 @@ |
24 | 24 |
- <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211> |
25 | 25 |
|
26 | 26 |
--> |
27 |
-# ggtree 3.5.2.991 |
|
27 |
+# ggtree 3.5.2.992 |
|
28 | 28 |
|
29 |
++ update `fortify` method for `pvclust` object (2022-08-15, Mon) |
|
29 | 30 |
+ add citation of the tree data book (2022-08-13, Sat) |
30 | 31 |
|
31 | 32 |
# ggtree 3.5.2 |
... | ... |
@@ -25,8 +25,10 @@ |
25 | 25 |
|
26 | 26 |
--> |
27 | 27 |
|
28 |
-# ggtree 3.5.1.902 |
|
28 |
+# ggtree 3.5.2 |
|
29 | 29 |
|
30 |
++ `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) |
... | ... |
@@ -25,10 +25,11 @@ |
25 | 25 |
|
26 | 26 |
--> |
27 | 27 |
|
28 |
-# ggtree 3.5.1.901 |
|
28 |
+# ggtree 3.5.1.902 |
|
29 | 29 |
|
30 |
++ 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) |
31 |
-+ optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu) |
|
32 |
++ optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu, #508) |
|
32 | 33 |
|
33 | 34 |
# ggtree 3.5.1 |
34 | 35 |
|
... | ... |
@@ -25,6 +25,10 @@ |
25 | 25 |
|
26 | 26 |
--> |
27 | 27 |
|
28 |
+# ggtree 3.5.1.900 |
|
29 |
+ |
|
30 |
++ optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu) |
|
31 |
+ |
|
28 | 32 |
# ggtree 3.5.1 |
29 | 33 |
|
30 | 34 |
+ `as.phylo.hclust2` to correct edge length as displayed in `stats:::plot.hclust` (2022-06-21, Tue) |
... | ... |
@@ -25,10 +25,10 @@ |
25 | 25 |
|
26 | 26 |
--> |
27 | 27 |
|
28 |
-# ggtree 3.5.0.902 |
|
28 |
+# ggtree 3.5.1 |
|
29 | 29 |
|
30 |
++ `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 |
|
... | ... |
@@ -25,8 +25,9 @@ |
25 | 25 |
|
26 | 26 |
--> |
27 | 27 |
|
28 |
-# ggtree 3.5.0.901 |
|
28 |
+# ggtree 3.5.0.902 |
|
29 | 29 |
|
30 |
++ 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'` |
... | ... |
@@ -25,8 +25,9 @@ |
25 | 25 |
|
26 | 26 |
--> |
27 | 27 |
|
28 |
-# ggtree 3.5.0.900 |
|
28 |
+# ggtree 3.5.0.901 |
|
29 | 29 |
|
30 |
++ `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 |
|
... | ... |
@@ -25,6 +25,15 @@ |
25 | 25 |
|
26 | 26 |
--> |
27 | 27 |
|
28 |
+# ggtree 3.5.0.900 |
|
29 |
+ |
|
30 |
++ new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497) |
|
31 |
+ - only works for Cartesian coordination, that means it will not work for `layout = 'radial'` |
|
32 |
+ |
|
33 |
+# ggtree 3.4.0 |
|
34 |
+ |
|
35 |
++ Bioconductor 3.15 release (2022-04-28, Thu) |
|
36 |
+ |
|
28 | 37 |
# ggtree 3.3.3 |
29 | 38 |
|
30 | 39 |
+ `geom_striplab()` that supports `aes()` mapping (2022-04-22, Fri, #493) |
... | ... |
@@ -25,6 +25,11 @@ |
25 | 25 |
|
26 | 26 |
--> |
27 | 27 |
|
28 |
+# ggtree 3.3.3 |
|
29 |
+ |
|
30 |
++ `geom_striplab()` that supports `aes()` mapping (2022-04-22, Fri, #493) |
|
31 |
++ `to.bottom` parameter introduced in `geom_hilight()` to allow the highlight layer was added into the lowest layer stack (2022-04-22, Fri, #492) |
|
32 |
+ |
|
28 | 33 |
# ggtree 3.3.2 |
29 | 34 |
|
30 | 35 |
+ mv `identify()` method to 'ggfun' (2022-04-01, Fri) |
... | ... |
@@ -27,7 +27,8 @@ |
27 | 27 |
|
28 | 28 |
# ggtree 3.3.1.901 |
29 | 29 |
|
30 |
-+ update `identify.gg()` to support 'ggplot' object and `+xlim()` (2022-04-01, Fri) |
|
30 |
++ mv `identify()` method to 'ggfun' (2022-04-01, Fri) |
|
31 |
++ update `identify.gg()` to support 'ggplot' object and `+xlim()` |
|
31 | 32 |
+ update man files (2022-03-23, Wed, #489) |
32 | 33 |
|
33 | 34 |
# ggtree 3.3.1 |
... | ... |
@@ -20,12 +20,15 @@ |
20 | 20 |
- <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> |
26 | 25 |
|
27 | 26 |
--> |
28 | 27 |
|
28 |
+# ggtree 3.3.1.900 |
|
29 |
+ |
|
30 |
++ update man files (2022-03-23, Wed, #489) |
|
31 |
+ |
|
29 | 32 |
# ggtree 3.3.1 |
30 | 33 |
|
31 | 34 |
+ use graph layouts to visualize tree (2021-12-10, Fri, #460, #461) |
... | ... |
@@ -2,11 +2,8 @@ |
2 | 2 |
|
3 | 3 |
# TODO LIST |
4 | 4 |
|
5 |
-+ use graph layout to visualize tree |
|
6 |
- - <https://github.com/YuLab-SMU/ggtree/issues/460> |
|
7 |
- + 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` |
... | ... |
@@ -29,8 +26,11 @@ |
29 | 26 |
|
30 | 27 |
--> |
31 | 28 |
|
32 |
-# ggtree 3.3.0.901 |
|
33 |
- |
|
29 |
+# ggtree 3.3.1 |
|
30 |
+ |
|
31 |
++ use graph layouts to visualize tree (2021-12-10, Fri, #460, #461) |
|
32 |
+ - 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) |
36 | 36 |
|
... | ... |
@@ -2,6 +2,11 @@ |
2 | 2 |
|
3 | 3 |
# TODO LIST |
4 | 4 |
|
5 |
++ use graph layout to visualize tree |
|
6 |
+ - <https://github.com/YuLab-SMU/ggtree/issues/460> |
|
7 |
+ + igraph layout |
|
8 |
+ + 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` |
... | ... |
@@ -26,7 +26,7 @@ |
26 | 26 |
|
27 | 27 |
# ggtree 3.3.0.901 |
28 | 28 |
|
29 |
-+ `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) |
31 | 31 |
|
32 | 32 |
# ggtree 3.2.0 |
... | ... |
@@ -24,8 +24,9 @@ |
24 | 24 |
|
25 | 25 |
--> |
26 | 26 |
|
27 |
-# ggtree 3.3.0.900 |
|
27 |
+# ggtree 3.3.0.901 |
|
28 | 28 |
|
29 |
++ `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) |
30 | 31 |
|
31 | 32 |
# ggtree 3.2.0 |
... | ... |
@@ -2,6 +2,8 @@ |
2 | 2 |
|
3 | 3 |
# TODO LIST |
4 | 4 |
|
5 |
++ `phylogeography` |
|
6 |
+ - <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> |
... | ... |
@@ -3,8 +3,10 @@ |
3 | 3 |
# TODO LIST |
4 | 4 |
|
5 | 5 |
+ `phylomorphospace` |
6 |
-+ `type` parameter in `geom_hilight` accepts 'roundrect' and 'gradient' |
|
7 |
- - <https://github.com/YuLab-SMU/ggtree/pull/444#issuecomment-949335277> |
|
6 |
+ - <https://github.com/YuLab-SMU/ggtree/issues/370> |
|
7 |
+ - <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` |
... | ... |
@@ -2,6 +2,8 @@ |
2 | 2 |
|
3 | 3 |
# TODO LIST |
4 | 4 |
|
5 |
++ `type` parameter in `geom_hilight` accepts 'roundrect' and 'gradient' |
|
6 |
+ - <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> |
7 | 9 |
+ rewrite `revts` to `scale_revts` |
... | ... |
@@ -21,7 +23,7 @@ |
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 |
... | ... |
@@ -19,7 +19,7 @@ |
19 | 19 |
--> |
20 | 20 |
|
21 | 21 |
|
22 |
-# ggtree 3.1.5.902 |
|
22 |
+# ggtree 3.1.6 |
|
23 | 23 |
|
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) |
... | ... |
@@ -4,6 +4,8 @@ |
4 | 4 |
|
5 | 5 |
+ `height` parameter to `collapse()` |
6 | 6 |
- <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> |
... | ... |
@@ -12,11 +14,6 @@ |
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 |
|
... | ... |
@@ -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> |
... | ... |
@@ -1,3 +1,5 @@ |
1 |
+<!-- |
|
2 |
+ |
|
1 | 3 |
# TODO LIST |
2 | 4 |
|
3 | 5 |
+ tanglegram support |
... | ... |
@@ -12,10 +14,14 @@ |
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 |
|
... | ... |
@@ -14,9 +14,10 @@ |
14 | 14 |
- <https://developer.r-project.org/Blog/public/2020/07/15/new-features-in-the-r-graphics-engine/> |
15 | 15 |
|
16 | 16 |
|
17 |
-# 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 |
|
... | ... |
@@ -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 |
|
... | ... |
@@ -10,6 +10,9 @@ |
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 |
|
... | ... |
@@ -11,9 +11,9 @@ |
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 |
|
... | ... |
@@ -1,5 +1,19 @@ |
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 |
|
... | ... |
@@ -1,5 +1,6 @@ |
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) |
... | ... |
@@ -1,5 +1,6 @@ |
1 |
-# 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 |
|
... | ... |
@@ -1,5 +1,6 @@ |
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 |
... | ... |
@@ -1,3 +1,7 @@ |
1 |
+# 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) |
... | ... |
@@ -1,5 +1,6 @@ |
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) |
... | ... |
@@ -1,5 +1,7 @@ |
1 |
-# 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 |
... | ... |
@@ -1,5 +1,7 @@ |
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())` |
... | ... |
@@ -1,4 +1,15 @@ |
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 |
|
... | ... |
@@ -1,3 +1,7 @@ |
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) |
... | ... |
@@ -1,7 +1,8 @@ |
1 |
-# 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 |
|
... | ... |
@@ -1,5 +1,7 @@ |
1 |
-# 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 |
|
... | ... |
@@ -1,3 +1,8 @@ |
1 |
+# 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) |
... | ... |
@@ -1,5 +1,6 @@ |
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) |
... | ... |
@@ -1,5 +1,9 @@ |
1 |
-# 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> |
... | ... |
@@ -1,5 +1,8 @@ |
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 |
|
... | ... |
@@ -1,3 +1,9 @@ |
1 |
+# 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` |
... | ... |
@@ -1,5 +1,8 @@ |
1 |
-# ggtree 2.3.5.993 |
|
1 |
+# 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) |
... | ... |
@@ -1,5 +1,6 @@ |
1 |
-# 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> |
... | ... |
@@ -1,6 +1,7 @@ |
1 |
-# ggtree 2.3.5.991 |
|
1 |
+# 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 |
... | ... |
@@ -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) |
... | ... |
@@ -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 |
|
... | ... |
@@ -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) |
... | ... |
@@ -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 |
|
... | ... |
@@ -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 |
|
... | ... |
@@ -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 |
|
... | ... |
@@ -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 |
... | ... |
@@ -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) |
... | ... |
@@ -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. |
... | ... |
@@ -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) |
... | ... |
@@ -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 |
... | ... |
@@ -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 |
... | ... |
@@ -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 |
... | ... |
@@ -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) |
... | ... |
@@ -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 |
|
... | ... |
@@ -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 |
... | ... |
@@ -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`, |
... | ... |
@@ -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 |
... | ... |
@@ -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) |
... | ... |
@@ -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) |
... | ... |
@@ -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 |
|
... | ... |
@@ -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 |
... | ... |
@@ -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` |
... | ... |
@@ -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) |
... | ... |
@@ -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> |
... | ... |
@@ -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) |
... | ... |
@@ -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) |
... | ... |
@@ -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) |
... | ... |
@@ -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 |
|
... | ... |
@@ -1,3 +1,11 @@ |
1 |
+# ggtree 2.1.2 |
|
2 |
+ |
|
3 |
++ bug fixed of determined layout for `ggplot(tree) + geom_tiplab()` (2020-01-26, Sun) |
|
4 |
+ - <https://github.com/YuLab-SMU/ggtree/issues/272> |
|
5 |
++ set unrooted layout to use `coord_fixed` by default (2020-01-25, Sat) |
|
6 |
++ if `layout = "ape"`, use ape unrooted layout |
|
7 |
+ - <https://github.com/YuLab-SMU/ggtree/issues/272> |
|
8 |
+ |
|
1 | 9 |
# ggtree 2.1.1 |
2 | 10 |
|
3 | 11 |
+ export `geom_highlight` as an alias of `geom_hilight` (2020-01-08, Wed) |
... | ... |
@@ -1,5 +1,6 @@ |
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` |
... | ... |
@@ -1,5 +1,6 @@ |
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) |
... | ... |
@@ -1,5 +1,7 @@ |
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) |
... | ... |
@@ -1,5 +1,6 @@ |
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) |
... | ... |
@@ -1,6 +1,7 @@ |
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> |
... | ... |
@@ -1,7 +1,7 @@ |
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) |
|
4 |
++ `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) |
... | ... |
@@ -1,7 +1,9 @@ |
1 | 1 |
# 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) |
|
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) |
|
4 | 5 |
- <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot> |
6 |
+ - <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 |
|
... | ... |
@@ -1,6 +1,6 @@ |
1 | 1 |
# 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> |
... | ... |
@@ -1,5 +1,7 @@ |
1 | 1 |
# 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) |
|
4 |
+ - <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 |
|
... | ... |
@@ -1,3 +1,12 @@ |
1 |
+# ggtree 2.1.1 |
|
2 |
+ |
|
3 |
++ fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed) |
|
4 |
+ - <https://github.com/YuLab-SMU/ggtree/issues/260> |
|
5 |
+ |
|
6 |
+# ggtree 2.0.0 |
|
7 |
+ |
|
8 |
++ Bioconductor 3.10 release (2019-10-30, Wed) |
|
9 |
+ |
|
1 | 10 |
# ggtree 1.99.1 |
2 | 11 |
|
3 | 12 |
+ bug fixed of `geom_hilight` for `tree$edge.length = NULL` (2019-10-16, Wed) |
... | ... |
@@ -1,5 +1,7 @@ |
1 | 1 |
# ggtree 1.99.1 |
2 | 2 |
|
3 |
++ bug fixed of `geom_hilight` for `tree$edge.length = NULL` (2019-10-16, Wed) |
|
4 |
+ - <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> |
... | ... |
@@ -2,7 +2,9 @@ |
2 | 2 |
|
3 | 3 |
+ `ggdensitree` (2019-09-11, Wed) |
4 | 4 |
- <https://github.com/YuLab-SMU/ggtree/pull/253> |
5 |
- |
|
5 |
+ - <https://github.com/YuLab-SMU/ggtree/pull/255> |
|
6 |
+ - <https://yulab-smu.github.io/treedata-book/chapter4.html#visualize-a-list-of-trees> |
|
7 |
+ |
|
6 | 8 |
# ggtree 1.99.0 |
7 | 9 |
|
8 | 10 |
+ prepare for ggtree v=2.0.0 |
... | ... |
@@ -11,6 +13,7 @@ |
11 | 13 |
|
12 | 14 |
+ `fortify` methods for hierarchical clustering objects, including `agnes`, `diana` and `twins` (2019-08-30, Fri) |
13 | 15 |
+ now `geom_hilight` supports `unrooted` and `daylight` layouts (2019-08-28, Wed) |
16 |
+ - by calling `geom_hilight_encircle` |
|
14 | 17 |
+ update `geom_motif` according to the change of `gggenes` and allow labeling genes (2019-08-27, Tue) |
15 | 18 |
- <https://yulab-smu.github.io/treedata-book/chapter11.html#genome-locus> |
16 | 19 |
+ re-implement `geom_strip` with more robust support of labelling strip, either input taxa using name or id. |