Doublet detection

VERSION

@@ -1 +1 @@
-0.28.8
+0.29.0

scarf/datastore/datastore.py

@@ -1,13 +1,16 @@
 from typing import Iterable, Optional, Union, List, Literal, Tuple
+
 import numpy as np
 import pandas as pd
 from dask import array as daskarr
 from loguru import logger
+
 from .mapping_datastore import MappingDatastore
-from ..writers import create_zarr_obj_array, create_zarr_dataset
-from ..utils import tqdmbar, controlled_compute, ZARRLOC
+from .. import doublet_scoring
 from ..assay import RNAassay, ATACassay
 from ..feat_utils import hto_demux
+from ..utils import tqdmbar, controlled_compute, ZARRLOC
+from ..writers import create_zarr_obj_array, create_zarr_dataset
 
 __all__ = ["DataStore"]
 
@@ -1208,6 +1211,44 @@ def smart_label(
         else:
             self.cells.insert(new_col_name, ret_val, overwrite=True)
 
+    def predict_doublet_score(
+        self, sim_doublet_ratio: float = 2, smoothen_iteration: int = 2
+    ):
+        idx = doublet_scoring.get_simulated_pair_idx(
+            self.cells.fetch_all("I").sum(), sim_doublet_ratio=sim_doublet_ratio
+        )
+        simulated_doublets = doublet_scoring.get_simulated_doublets(self, idx)
+
+        # TODO: what should be the sim_dset_path
+        doublet_scoring.save_sim_doublets(
+            simulated_doublets, assay=self.RNA, idx=idx, sim_dset_path="workspace"
+        )
+        sim_ds = DataStore("workspace")
+        doublet_scoring.process_sim_ds(sim_ds)
+        self.run_mapping(
+            target_assay=sim_ds.RNA,
+            target_name="sim_ds",
+            target_feat_key="hvgs_ctrl",
+            save_k=11,
+            run_coral=False,
+        )
+
+        # TODO:  is this correct way of fetching?
+        _, ms = next(
+            self.get_mapping_score(
+                target_name="sim_ds", log_transform=False, multiplier=1e4
+            )
+        )
+
+        graph = self.load_graph()
+        doublet_scores = doublet_scoring.average_signal_by_neighbour(
+            graph.indices.reshape(graph.shape[0], 11).astype("int64"),
+            graph.data.reshape(graph.shape[0], 11).astype("float64"),
+            ms.astype("float64"),
+            t=smoothen_iteration,
+        )
+        self.cells.insert("doublet_scores", doublet_scores, overwrite=True)
+
     def plot_cells_dists(
         self,
         from_assay: Optional[str] = None,

scarf/doublet_scoring.py

@@ -0,0 +1,111 @@
+import numpy as np
+import pandas as pd
+import zarr
+from numba import jit
+
+from .utils import tqdmbar
+from .writers import create_zarr_count_assay, create_cell_data
+
+
+def get_simulated_pair_idx(
+    n_obs: int,
+    random_seed: int = 1,
+    sim_doublet_ratio: float = 2.0,
+    cell_range: int = 100,
+):
+    """
+    sim_doublet_ratio: ratio of simulated doublets. Default 2
+    """
+    n_sim = int(n_obs * sim_doublet_ratio)
+
+    rng_state = np.random.RandomState(random_seed)
+    pair_1 = rng_state.randint(0, n_obs, size=n_sim)
+    # If we assume that the order of cells (indices) is truly random in the source dataset ie iid
+    # Then it doesn't matter what the search space for random cell is
+    pair_2 = np.array(
+        [
+            rng_state.randint(
+                max(0, x - cell_range), min(n_obs - 1, x + cell_range), size=1
+            )[0]
+            for x in pair_1
+        ]
+    )
+
+    idx = np.array([pair_1, pair_2]).T
+    idx = pd.DataFrame(idx).sort_values(by=[0, 1]).values
+
+    return idx
+
+
+def get_simulated_doublets(ds, indexes: np.ndarray):
+    return ds.RNA.rawData[indexes[:, 0]] + ds.RNA.rawData[indexes[:, 1]]
+
+
+def save_sim_doublets(
+    simulated_doublets, assay, idx, sim_dset_path: str, rechunk=False
+) -> None:
+    zarr_path = zarr.open(sim_dset_path, "w")
+
+    g = create_zarr_count_assay(
+        z=zarr_path,
+        assay_name=assay.name,
+        workspace=None,
+        chunk_size=assay.rawData.chunksize,
+        n_cells=simulated_doublets.shape[0],
+        feat_ids=assay.feats.fetch_all("ids"),
+        feat_names=assay.feats.fetch_all("names"),
+    )
+    sim_cell_ids = np.array([f"Sim_{x[0]}-{x[1]}" for x in idx]).astype(object)
+    create_cell_data(z=zarr_path, workspace=None, ids=sim_cell_ids, names=sim_cell_ids)
+    if rechunk:
+        simulated_doublets = simulated_doublets.rechunk(
+            1000, simulated_doublets.shape[1]
+        )
+
+    compute_write(simulated_doublets, g)
+
+
+# TODO: is there built-in scarf function to replace this
+def compute_write(simulated, zarr_array):
+    s, e = 0, 0
+    batch = None
+
+    # TODO: do we need tqdm here
+    for i in tqdmbar(simulated.blocks, total=simulated.numblocks[0]):
+        if batch is None:
+            batch = i.compute()
+        else:
+            batch = np.vstack([batch, i.compute()])
+        if len(batch) > 1000:
+            e += batch.shape[0]
+            zarr_array[s:e] = batch
+            batch = None
+            s = e
+
+    if batch is not None:
+        e += batch.shape[0]
+        zarr_array[s:e] = batch
+
+    assert e == simulated.shape[0]
+
+
+@jit(cache=True, nopython=True)
+def average_signal_by_neighbour(inds, data, signal, t: int):
+    out = signal.copy()
+    n = out.shape[0]
+    for _ in range(t):
+        temp = np.zeros(n)
+        for i in range(n):
+            neighbour_w_mean = (out[inds[i]] * data[i]).mean()
+            temp[i] = (out[i] + neighbour_w_mean) / 2
+        out = temp.copy()
+
+    return out
+
+
+def process_sim_ds(sim_ds):
+    sim_ds.mark_hvgs(min_cells=20, top_n=500, min_mean=-3, max_mean=2, max_var=6)
+
+    sim_ds.make_graph(
+        feat_key="hvgs", k=11, dims=15, n_centroids=100, local_connectivity=0.9
+    )