Skip to content

Changed: Update README to show newick export examples #145

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
kayjan merged 1 commit into from
Jan 2, 2024
Merged

Changed: Update README to show newick export examples #145

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 13 additions & 8 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ For **Tree** implementation, there are 9 main components.
1. Enhanced Reingold Tilford Algorithm to retrieve (x, y) coordinates for a tree structure
8. [**🔨 Exporting Tree**](https://bigtree.readthedocs.io/en/latest/bigtree/tree/export.html)
1. Print to console
2. Export to *dictionary*, *nested dictionary*, or *pandas DataFrame*
2. Export to *Newick string notation*, *dictionary*, *nested dictionary*, or *pandas DataFrame*
3. Export tree to *dot* (can save to .dot, .png, .svg, .jpeg files)
4. Export tree to *Pillow* (can save to .png, .jpg)
5. Export tree to *Mermaid Flowchart* (can display on .md)
Expand Down Expand Up @@ -864,21 +864,23 @@ tree_diff.show()

Tree can be exported to another data type.

1. *Export to **nested dictionary***
2. *Export to **nested recursive dictionary***
3. *Export to **pandas DataFrame***
4. *Export to **dot** (and png)*
5. *Export to **Pillow** (and png)*
6. *Export to **Mermaid Flowchart** (and md)*
1. *Export to **Newick string notation***
2. *Export to **nested dictionary***
3. *Export to **nested recursive dictionary***
4. *Export to **pandas DataFrame***
5. *Export to **dot** (and png)*
6. *Export to **Pillow** (and png)*
7. *Export to **Mermaid Flowchart** (and md)*

{emphasize-lines="23-28,37,63-69,77,80,83"}
{emphasize-lines="24, 27-32,41,67-73,81,84,87"}
```python
from bigtree import (
Node,
tree_to_dataframe,
tree_to_dict,
tree_to_dot,
tree_to_mermaid,
tree_to_newick,
tree_to_nested_dict,
tree_to_pillow,
)
Expand All @@ -895,6 +897,9 @@ root.show()
# │ └── e
# └── c

tree_to_newick(root)
# '((d,e)b,c)a'

tree_to_dict(
root,
name_key="name",
Expand Down