hierdiff
A package that is useful for clustering high-dimensional instances (e.g. T cell receptors) and testing whether clusters of instances are differentially abundant in two or more categorical conditions. The package provides d3/SVG rendering of scipy hierarchical clustering dendrograms with zooming, panning and tooltips. This uniquely allows for exploring large trees of datasets, conditioned on a categorical trait.
Installation
pip install hierdiff
Example
import hierdiff
from scipy.spatial.distance import squareform
"""Contains categorical variable column 'trait1' and
instance counts in 'count'"""
dat, pwdist = generate_data()
res, Z = hierdiff.hcluster_tally(dat,
pwmat=squareform(pwdist),
x_cols=['trait1'],
count_col='count',
method='complete')
res = hierdiff.cluster_association_test(res, method='fishers')
"""Plot frequency of trait at nodes with p-value < 0.05"""
html = plot_hclust_props(Z, title='test_props2',
res=res, alpha=0.05, alpha_col='pvalue')
1 maintainer
Metadata
1 maintainer
Release files for hierdiff 0.85
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| hierdiff-0.85.tar.gz | 24.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| hierdiff-0.85-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 51.7 kB
Release files / hierdiff-0.85.tar.gz
| Download URL | hierdiff-0.85.tar.gz |
|---|---|
| Size | 24.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
2009a27e5e878b447bccbfa8981b715958fd7d6e29eae6ca473db2f35409298a
|
|
BLAKE2b-256 checksum How to use checksums |
a8e650b21c82dc08f6ed0390913916de4535f165f23e0a7b90de7ab631c283b3
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.0.0 CPython/3.11.5
|
Release files / hierdiff-0.85-py3-none-any.whl
| Download URL | hierdiff-0.85-py3-none-any.whl |
|---|---|
| Size | 27.3 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
94672c639e6007c1adf1ecd8e9d707dfe37af218859fb50e0078a783bc4533e1
|
|
BLAKE2b-256 checksum How to use checksums |
92604c30b5dce11db9b8533fc639b8993ebc00fb86a6f658bede5cf112324383
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.0.0 CPython/3.11.5
|
