Merge branch 'feat/tcrdist' into 'master'

Feat/tcrdist

Closes #11

See merge request icbi-lab/pipelines/singlecell_tcr!10

pyproject.toml

@@ -23,7 +23,8 @@ requires = [
     # pandas <1 until scanpy is fully compatible...
     'pandas<1',
     'numpy',
-    'parasail'
+    'parasail',
+    'scikit-learn'
 ]
 
 [tool.flit.metadata.requires-extra]

sctcrpy/_plotting/_plots.py

@@ -9,6 +9,7 @@
 from . import _base as base
 from typing import Union, List
 from ._styling import _check_for_plotting_profile
+import scanpy as sc
 
 
 def alpha_diversity(
@@ -600,3 +601,11 @@ def group_abundance(
         main_args = dict(dict(profile_args, **plot_router[viztype]["arg"]), **vizarg)
         axl = plot_router[viztype]["f"](**main_args)
         return axl
+
+
+def umap_tra(adata: AnnData, **kwargs):
+    return sc.pl.embedding(adata, "X_umap_tra", **kwargs)
+
+
+def umap_trb(adata: AnnData, **kwargs):
+    return sc.pl.embedding(adata, "X_umap_trb", **kwargs)

sctcrpy/_preprocessing.py

@@ -1,6 +1,4 @@
-import pandas as pd
 from typing import Union, List
-import numpy as np
 from anndata import AnnData
 
 

sctcrpy/_tools/__init__.py

@@ -1 +1,2 @@
 from ._tools import *
+from ._tcr_dist import tcr_neighbors, tcr_umap