README.md

tiers

A hierarchical label handling library for Python

Installation

You can install tiers using pip:

pip install git+https://github.com/mikkoim/tiers.git

For the latest version, install the dev branch:

pip install https://github.com/mikkoim/tiers/archive/dev.zip

Examples

See the demo notebook for more details.

Creating a tiers Tree from a Pandas DataFrame:

import pandas as pd
from tiers import Tree

# Sample DataFrame with hierarchical data
data = {
    "Level1": ["A", "A", "B", "B", "B"],
    "Level2": ["A1", "A2", None, "B2", "B3"],
    "Level3": ["A1a", "A2b", None, None, "B3c"],
    "Label": ["Label1", "Label2", "Label3", "Label4", "Label5"]
}
df = pd.DataFrame(data)

# Create a Tree object from the DataFrame
tree = Tree.from_dataframe(df, set_root=True)

# Show the tree
tree.show()
# root
# ├── A
# │   ├── A1
# │   │   └── A1a
# │   └── A2
# │       └── A2b
# └── B
#     ├── B2
#     └── B3
#         └── B3c

Mapping labels to nodes at a specific level

# Map labels to nodes at a specific level
mapped_nodes = tree.map(["Label1", "Label2", "Label3", "Label4", "Label5"],
                        level="Level2")
print(mapped_nodes)  # Output: ['A1', 'A2', 'B', 'B2', 'B3']

# Mapping can be also done stricty on specific level
level3_labels = tree.map(["Label5", "Label4", "Label3"],
                        level="Level3",
                        strict=True)
print(level3_labels) # Output: ['B3c', None, None]

Setting the tree to a level and mapping labels to it

tree.set_level("Level1")
mapped_nodes = tree.map(["Label1", "Label2", "Label3", "Label4", "Label5"])
print(mapped_nodes) # Output: ['A', 'A', 'B', 'B', 'B']

Regrouping pandas dataframes

level="order"
grouped = df.assign(taxon=tree.map(df.index, level=level)).groupby("taxon").sum()

Extending a label into a pandas.MultiIndex is also supported.

Extending formatted label strings for plotting

import matplotlib.pyplot as plt
plt.rcParams["font.family"] = "monospace" # Make labels align properly
df = df.loc[tree.sort_labels(df.index)] # Sort the labels based on the hierarchical order

fig, ax = plt.subplots()
ax.matshow(df) 

# Tiers works here. Padding is set automatically:
extended_labels = tree.extend_labels(df.index, return_string=True, pad=True)

# Set the labels
ax.set_yticks(range(len(df.index)), # Tick locations
              labels=extended_labels)
plt.show()

Subsets of columns can also be selected.

Finding the Lowest Common Ancestor for two nodes:

# Find the Lowest Common Ancestor (LCA) of two nodes
print(tree.lca("Label2", "Label4")) # Output: 'root'
print(tree.lca("Label1", "Label2")) # Output: 'A'

See the demo notebook for more details.

Acknowledgements

This library uses the excellent bigtree library, which provides support for handling tree structures.

Contributing

Contributions are welcome! If you encounter any issues or have suggestions for improvements, please feel free to open an issue or submit a pull request. The library is still under heavy development and breaking changes can be introduced.