deleted file mode 100644

@@ -1,19 +0,0 @@

-# TODO LIST

-

-+ tanglegram support

-  - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

-  - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo> 

-+ `fortify` method for `phyloseq` object should return a tidy data.frame

-  - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`

-+ update ggtree man files

-+ The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

-  - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

-+ ~~mplement quarter ellipse layout to draw tree~~

-+ ~~A new geom, `geom_cladelab`, that supports aes mapping and the parameter `horizontal` works for all layouts~~

-  - <https://github.com/YuLab-SMU/ggtree/pull/342>

-  - extend `geom_cladelabel` to support aes mapping

-  - `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`

-+ ~~update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`~~

-   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

-   - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>

-   - <https://github.com/YuLab-SMU/ggtree/pull/341>

@@ -2,6 +2,7 @@

 + tanglegram support

   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

+  - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo> 

 + `fortify` method for `phyloseq` object should return a tidy data.frame

   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`

 + update ggtree man files

@@ -1,18 +1,18 @@

 # TODO LIST

-+ [ ] tanglegram support

++ tanglegram support

   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

-+ [ ] `fortify` method for `phyloseq` object should return a tidy data.frame

++ `fortify` method for `phyloseq` object should return a tidy data.frame

   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`

-+ [ ] update ggtree man files

-+ [ ] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

++ update ggtree man files

++ The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

-+ [ ] Implement quarter ellipse layout to draw tree

-+ [x] A new geom, `geom_cladelab`, that supports aes mapping and the parameter `horizontal` works for all layouts (2020-09-17, Thu)

++ ~~mplement quarter ellipse layout to draw tree~~

++ ~~A new geom, `geom_cladelab`, that supports aes mapping and the parameter `horizontal` works for all layouts~~

   - <https://github.com/YuLab-SMU/ggtree/pull/342>

   - extend `geom_cladelabel` to support aes mapping

   - `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`

-+ [x] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)

++ ~~update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`~~

    - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

    - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>

    - <https://github.com/YuLab-SMU/ggtree/pull/341>

@@ -1,16 +1,18 @@

 # TODO LIST

-+ tanglegram support

++ [ ] tanglegram support

   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

 + [ ] `fortify` method for `phyloseq` object should return a tidy data.frame

   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`

 + [ ] update ggtree man files

-+ [ ] extend `geom_cladelabel` to support aes mapping   

-+ [ ] `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`

 + [ ] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

-   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

+  - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

 + [ ] Implement quarter ellipse layout to draw tree

++ [x] A new geom, `geom_cladelab`, that supports aes mapping and the parameter `horizontal` works for all layouts (2020-09-17, Thu)

+  - <https://github.com/YuLab-SMU/ggtree/pull/342>

+  - extend `geom_cladelabel` to support aes mapping

+  - `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`

 + [x] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)

    - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

    - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>

-   - <https://github.com/YuLab-SMU/ggtree/pull/341>

\ No newline at end of file

+   - <https://github.com/YuLab-SMU/ggtree/pull/341>

@@ -1,5 +1,7 @@

 # TODO LIST

++ tanglegram support

+  - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

 + [ ] `fortify` method for `phyloseq` object should return a tidy data.frame

   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`

 + [ ] update ggtree man files

@@ -1,7 +1,7 @@

 # TODO LIST

 + [ ] `fortify` method for `phyloseq` object should return a tidy data.frame

-  - maybe we can defined another object and provide converter for `phyloseq`

+  - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`

 + [ ] update ggtree man files

 + [ ] extend `geom_cladelabel` to support aes mapping   

 + [ ] `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`

@@ -1,6 +1,8 @@

 # TODO LIST

-+ [ ]update ggtree man files

++ [ ] `fortify` method for `phyloseq` object should return a tidy data.frame

+  - maybe we can defined another object and provide converter for `phyloseq`

++ [ ] update ggtree man files

 + [ ] extend `geom_cladelabel` to support aes mapping   

 + [ ] `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`

 + [ ] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

@@ -1,11 +1,12 @@

 # TODO LIST

-+ update ggtree man files

-+ [] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`

++ [ ]update ggtree man files

++ [ ] extend `geom_cladelabel` to support aes mapping   

++ [ ] `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`

++ [ ] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

+   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

++ [ ] Implement quarter ellipse layout to draw tree

++ [x] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)

    - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

    - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>

-+ [] extend `geom_cladelabel` to support aes mapping   

-+ [] `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`

-+ [] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

-   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

-+ [] Implement quarter ellipse layout to draw tree

+   - <https://github.com/YuLab-SMU/ggtree/pull/341>

\ No newline at end of file

@@ -1,5 +1,11 @@

 # TODO LIST

++ update ggtree man files

 + [] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`

    - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

    - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>

++ [] extend `geom_cladelabel` to support aes mapping   

++ [] `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`

++ [] The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

+   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

++ [] Implement quarter ellipse layout to draw tree

new file mode 100644

@@ -0,0 +1,5 @@

+# TODO LIST

+

++ [] update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)`

+   - <https://yulab-smu.top/treedata-book/chapter2.html#ggtree-fortify>

+   - <https://groups.google.com/g/bioc-ggtree/c/swpAjXLZMOQ/m/igXf9crVBwAJ>

deleted file mode 100644

@@ -1,12 +0,0 @@

-+ attach user specific data to existing tree object

-+ attach user specific data by node number

-+ mask function that accepts tree object, feature name and a function that specific how to mask.

-  with this function, user can mask some of the features that are not needed to display on a tree.

-+ defined a function, compare_sequence, that accept a function that defined sequence feature,

-  and compare the feature from parent to children and add store the info in tree object.

-  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,

-  not only substitution supported internally.

-+ support more features that can be plotted at the right hand side of the tree.

-  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_

-  

-

new file mode 100644

@@ -0,0 +1,12 @@

++ attach user specific data to existing tree object

++ attach user specific data by node number

++ mask function that accepts tree object, feature name and a function that specific how to mask.

+  with this function, user can mask some of the features that are not needed to display on a tree.

++ defined a function, compare_sequence, that accept a function that defined sequence feature,

+  and compare the feature from parent to children and add store the info in tree object.

+  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,

+  not only substitution supported internally.

++ support more features that can be plotted at the right hand side of the tree.

+  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_

+  

+

deleted file mode 100644

@@ -1,12 +0,0 @@

-+ attach user specific data to existing tree object

-+ attach user specific data by node number

-+ mask function that accepts tree object, feature name and a function that specific how to mask.

-  with this function, user can mask some of the features that are not needed to display on a tree.

-+ defined a function, compare_sequence, that accept a function that defined sequence feature,

-  and compare the feature from parent to children and add store the info in tree object.

-  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,

-  not only substitution supported internally.

-+ support more features that can be plotted at the right hand side of the tree.

-  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_

-  

-

@@ -6,7 +6,7 @@

   and compare the feature from parent to children and add store the info in tree object.

   So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,

   not only substitution supported internally.

-+ support more features that can be plotted at the right hand side of the tree,

-  not only matrix but also for example sequence alignment or specific window of alignment.

++ support more features that can be plotted at the right hand side of the tree.

+  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_

new file mode 100644

@@ -0,0 +1,12 @@

++ attach user specific data to existing tree object

++ attach user specific data by node number

++ mask function that accepts tree object, feature name and a function that specific how to mask.

+  with this function, user can mask some of the features that are not needed to display on a tree.

++ defined a function, compare_sequence, that accept a function that defined sequence feature,

+  and compare the feature from parent to children and add store the info in tree object.

+  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,

+  not only substitution supported internally.

++ support more features that can be plotted at the right hand side of the tree,

+  not only matrix but also for example sequence alignment or specific window of alignment.

+  

+