Browse code

update docs

Guangchuang Yu authored on 27/09/2021 01:45:34
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1
-# TODO LIST
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
-+ ~~mplement quarter ellipse layout to draw tree~~
12
-+ ~~A new geom, `geom_cladelab`, that supports aes mapping and the parameter `horizontal` works for all layouts~~
13
-  - <https://github.com/YuLab-SMU/ggtree/pull/342>
14
-  - extend `geom_cladelabel` to support aes mapping
15
-  - `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
16
-+ ~~update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`~~
17
-   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
18
-   - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>
19
-   - <https://github.com/YuLab-SMU/ggtree/pull/341>
Browse code

bump up version

Guangchuang Yu authored on 10/10/2020 08:11:20
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@@ -2,6 +2,7 @@
2 2
 
3 3
 + tanglegram support
4 4
   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
5
+  - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo> 
5 6
 + `fortify` method for `phyloseq` object should return a tidy data.frame
6 7
   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`
7 8
 + update ggtree man files
Browse code

bump version up

Guangchuang Yu authored on 09/10/2020 03:09:26
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@@ -1,18 +1,18 @@
1 1
 # TODO LIST
2 2
 
3
-+ [ ] tanglegram support
3
++ tanglegram support
4 4
   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
5
-+ [ ] `fortify` method for `phyloseq` object should return a tidy data.frame
5
++ `fortify` method for `phyloseq` object should return a tidy data.frame
6 6
   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`
7
-+ [ ] update ggtree man files
8
-+ [ ] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
7
++ update ggtree man files
8
++ The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
9 9
   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
10
-+ [ ] Implement quarter ellipse layout to draw tree
11
-+ [x] A new geom, `geom_cladelab`, that supports aes mapping and the parameter `horizontal` works for all layouts (2020-09-17, Thu)
10
++ ~~mplement quarter ellipse layout to draw tree~~
11
++ ~~A new geom, `geom_cladelab`, that supports aes mapping and the parameter `horizontal` works for all layouts~~
12 12
   - <https://github.com/YuLab-SMU/ggtree/pull/342>
13 13
   - extend `geom_cladelabel` to support aes mapping
14 14
   - `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
15
-+ [x] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)
15
++ ~~update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`~~
16 16
    - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
17 17
    - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>
18 18
    - <https://github.com/YuLab-SMU/ggtree/pull/341>
Browse code

update docs

Guangchuang Yu authored on 17/09/2020 01:45:18
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@@ -1,16 +1,18 @@
1 1
 # TODO LIST
2 2
 
3
-+ tanglegram support
3
++ [ ] tanglegram support
4 4
   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
5 5
 + [ ] `fortify` method for `phyloseq` object should return a tidy data.frame
6 6
   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`
7 7
 + [ ] update ggtree man files
8
-+ [ ] extend `geom_cladelabel` to support aes mapping   
9
-+ [ ] `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
10 8
 + [ ] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
11
-   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
9
+  - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
12 10
 + [ ] Implement quarter ellipse layout to draw tree
11
++ [x] A new geom, `geom_cladelab`, that supports aes mapping and the parameter `horizontal` works for all layouts (2020-09-17, Thu)
12
+  - <https://github.com/YuLab-SMU/ggtree/pull/342>
13
+  - extend `geom_cladelabel` to support aes mapping
14
+  - `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
13 15
 + [x] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)
14 16
    - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
15 17
    - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>
16
-   - <https://github.com/YuLab-SMU/ggtree/pull/341>
17 18
\ No newline at end of file
19
+   - <https://github.com/YuLab-SMU/ggtree/pull/341>
Browse code

tanglegram

Guangchuang Yu authored on 14/09/2020 08:15:36
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@@ -1,5 +1,7 @@
1 1
 # TODO LIST
2 2
 
3
++ tanglegram support
4
+  - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
3 5
 + [ ] `fortify` method for `phyloseq` object should return a tidy data.frame
4 6
   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`
5 7
 + [ ] update ggtree man files
Browse code

treedata

Guangchuang Yu authored on 14/09/2020 02:24:21
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@@ -1,7 +1,7 @@
1 1
 # TODO LIST
2 2
 
3 3
 + [ ] `fortify` method for `phyloseq` object should return a tidy data.frame
4
-  - maybe we can defined another object and provide converter for `phyloseq`
4
+  - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`
5 5
 + [ ] update ggtree man files
6 6
 + [ ] extend `geom_cladelabel` to support aes mapping   
7 7
 + [ ] `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
Browse code

td_unnest

Guangchuang Yu authored on 14/09/2020 02:14:03
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@@ -1,6 +1,8 @@
1 1
 # TODO LIST
2 2
 
3
-+ [ ]update ggtree man files
3
++ [ ] `fortify` method for `phyloseq` object should return a tidy data.frame
4
+  - maybe we can defined another object and provide converter for `phyloseq`
5
++ [ ] update ggtree man files
4 6
 + [ ] extend `geom_cladelabel` to support aes mapping   
5 7
 + [ ] `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
6 8
 + [ ] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
Browse code

update docs

Guangchuang Yu authored on 03/09/2020 02:53:24
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@@ -1,11 +1,12 @@
1 1
 # TODO LIST
2 2
 
3
-+ update ggtree man files
4
-+ [] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`
3
++ [ ]update ggtree man files
4
++ [ ] extend `geom_cladelabel` to support aes mapping   
5
++ [ ] `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
6
++ [ ] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
7
+   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
8
++ [ ] Implement quarter ellipse layout to draw tree
9
++ [x] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)
5 10
    - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
6 11
    - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>
7
-+ [] extend `geom_cladelabel` to support aes mapping   
8
-+ [] `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
9
-+ [] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
10
-   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
11
-+ [] Implement quarter ellipse layout to draw tree
12
+   - <https://github.com/YuLab-SMU/ggtree/pull/341>
12 13
\ No newline at end of file
Guangchuang Yu authored on 02/09/2020 13:49:25
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@@ -1,5 +1,11 @@
1 1
 # TODO LIST
2 2
 
3
++ update ggtree man files
3 4
 + [] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`
4 5
    - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
5 6
    - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>
7
++ [] extend `geom_cladelabel` to support aes mapping   
8
++ [] `geom_cladelabel` internally calls `geom_cladelabel_rectangular` and `geom_cladelabel2`. The parameter `horizontal` introduced in `geom_cladelabel_retangular` should also be supported in `geom_cladelabel2`
9
++ [] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized
10
+   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>
11
++ [] Implement quarter ellipse layout to draw tree
Browse code

shadowtext

Guangchuang Yu authored on 02/09/2020 08:44:40
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@@ -0,0 +1,5 @@
1
+# TODO LIST
2
+
3
++ [] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`
4
+   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>
5
+   - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>
Browse code

rm todo

guangchuang yu authored on 09/03/2018 07:42:28
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1
-+ attach user specific data to existing tree object
2
-+ attach user specific data by node number
3
-+ mask function that accepts tree object, feature name and a function that specific how to mask.
4
-  with this function, user can mask some of the features that are not needed to display on a tree.
5
-+ defined a function, compare_sequence, that accept a function that defined sequence feature,
6
-  and compare the feature from parent to children and add store the info in tree object.
7
-  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,
8
-  not only substitution supported internally.
9
-+ support more features that can be plotted at the right hand side of the tree.
10
-  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_
11
-  
12
-
guangchuang yu authored on 11/10/2016 02:07:36
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@@ -0,0 +1,12 @@
1
++ attach user specific data to existing tree object
2
++ attach user specific data by node number
3
++ mask function that accepts tree object, feature name and a function that specific how to mask.
4
+  with this function, user can mask some of the features that are not needed to display on a tree.
5
++ defined a function, compare_sequence, that accept a function that defined sequence feature,
6
+  and compare the feature from parent to children and add store the info in tree object.
7
+  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,
8
+  not only substitution supported internally.
9
++ support more features that can be plotted at the right hand side of the tree.
10
+  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_
11
+  
12
+
Browse code

remove site

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122175 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 11/10/2016 02:01:09
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1 1
deleted file mode 100644
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@@ -1,12 +0,0 @@
1
-+ attach user specific data to existing tree object
2
-+ attach user specific data by node number
3
-+ mask function that accepts tree object, feature name and a function that specific how to mask.
4
-  with this function, user can mask some of the features that are not needed to display on a tree.
5
-+ defined a function, compare_sequence, that accept a function that defined sequence feature,
6
-  and compare the feature from parent to children and add store the info in tree object.
7
-  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,
8
-  not only substitution supported internally.
9
-+ support more features that can be plotted at the right hand side of the tree.
10
-  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_
11
-  
12
-
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 48b838ee337e94cff1f69151d75091b17bd7257f

msaplot


Commit id: 6083e201a71a1ff5ae2d11e635fb91e9e9c0b3fd

update appveyor.yml



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@104099 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 22/05/2015 08:47:09
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@@ -6,7 +6,7 @@
6 6
   and compare the feature from parent to children and add store the info in tree object.
7 7
   So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,
8 8
   not only substitution supported internally.
9
-+ support more features that can be plotted at the right hand side of the tree,
10
-  not only matrix but also for example sequence alignment or specific window of alignment.
9
++ support more features that can be plotted at the right hand side of the tree.
10
+  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_
11 11
   
12 12
 
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: f3f2f4065c71fc16952e75fed6b0d658ce467e03

TODO



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@104088 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 22/05/2015 04:01:16
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,12 @@
1
++ attach user specific data to existing tree object
2
++ attach user specific data by node number
3
++ mask function that accepts tree object, feature name and a function that specific how to mask.
4
+  with this function, user can mask some of the features that are not needed to display on a tree.
5
++ defined a function, compare_sequence, that accept a function that defined sequence feature,
6
+  and compare the feature from parent to children and add store the info in tree object.
7
+  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,
8
+  not only substitution supported internally.
9
++ support more features that can be plotted at the right hand side of the tree,
10
+  not only matrix but also for example sequence alignment or specific window of alignment.
11
+  
12
+