from collections import Counter
from typing import Optional
import numpy as np
import pandas as pd
from anndata import AnnData
from spatialtis_core import somde as smode_sv
from spatialtis.abc import AnalysisBase
from spatialtis.utils import read_points, doc
[docs]@doc
class somde(AnalysisBase):
"""This is a wrapper around somde
Args:
data: {adata}
k: Number of SOM nodes
alpha: Parameters for generate pseudo gene expression
epoch: Number of epoch
qval: Threshold for qval
pval: Threshold for pval
**kwargs: {analysis_kwargs}
"""
def __init__(
self,
data: AnnData,
k: int = 20,
alpha: float = 0.5,
epoch: int = 100,
pval: float = 0.05,
qval: float = 0.05,
**kwargs,
):
self.display_name = "SOMDE"
super().__init__(data, **kwargs)
track_ix = []
results_data = []
for roi_name, roi_data, markers, exp in self.roi_exp_iter(
desc="Spatial variable genes: SOMDE"
):
points = read_points(roi_data, self.centroid_key)
sv_genes = smode_sv(
pd.DataFrame(exp, index=markers, dtype=np.float32).fillna(0.0),
np.array(points, dtype=np.float32),
k=k, alpha=alpha, epoch=epoch, pval=pval, qval=qval
)
results_data.append(sv_genes)
track_ix.append(roi_name)
# a dict store all the markers
markers_dict = {k: 0 for k in self.markers}
# unpack and merge to ensure every counter has the same markers
self.result = pd.DataFrame(
data=[{**markers_dict, **Counter(i)} for i in results_data],
index=pd.MultiIndex.from_tuples(track_ix, names=self.exp_obs),
)[self.markers]
