sclab 0.2.5__tar.gz → 0.3.0__tar.gz

{sclab-0.2.5 → sclab-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sclab
-Version: 0.2.5
+Version: 0.3.0
 Summary: sclab
 Author-email: Argenis Arriojas <ArriojasMaldonado001@umb.edu>
 Requires-Python: >=3.10,<3.13
@@ -14,16 +14,19 @@ License-File: LICENSE
 Requires-Dist: anndata
 Requires-Dist: anywidget
 Requires-Dist: ipywidgets
-Requires-Dist: itables
+Requires-Dist: itables<2.4
 Requires-Dist: matplotlib
 Requires-Dist: numpy<2.2
 Requires-Dist: pandas
 Requires-Dist: plotly<6.0
 Requires-Dist: requests
+Requires-Dist: ripser>=0.6.12
 Requires-Dist: scikit-learn
 Requires-Dist: svgpathtools
 Requires-Dist: tqdm
 Requires-Dist: jupyterlab>=4.3.6 ; extra == "jupyter"
+Requires-Dist: anndata2ri>=1.3 ; extra == "r"
+Requires-Dist: rpy2>=3.5 ; extra == "r"
 Requires-Dist: scanpy[leiden, skmisc]>=1.10 ; extra == "scanpy"
 Requires-Dist: pytest>=8.3.4 ; extra == "test"
 Project-URL: Bug Tracker, https://github.com/umbibio/sclab/issues
@@ -32,6 +35,7 @@ Project-URL: Documentation, https://github.com/umbibio/sclab/docs
 Project-URL: Homepage, https://github.com/umbibio/sclab
 Project-URL: Repository, https://github.com/umbibio/sclab.git
 Provides-Extra: jupyter
+Provides-Extra: r
 Provides-Extra: scanpy
 Provides-Extra: test
 

{sclab-0.2.5 → sclab-0.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "sclab"
-version = "0.2.5"
+version = "0.3.0"
 description = "sclab"
 readme = "README.md"
 authors = [
@@ -18,12 +18,13 @@ dependencies = [
     "anndata",
     "anywidget",
     "ipywidgets",
-    "itables",
+    "itables<2.4",
     "matplotlib",
     "numpy<2.2",
     "pandas",
     "plotly<6.0",
     "requests",
+    "ripser>=0.6.12",
     "scikit-learn",
     "svgpathtools",
     "tqdm",
@@ -37,9 +38,10 @@ dependencies = [
 "Changelog" = "https://github.com/umbibio/sclab/blob/main/CHANGELOG.md"
 
 [project.optional-dependencies]
-test = ["pytest>=8.3.4"]
-scanpy = ["scanpy[leiden,skmisc]>=1.10"]
 jupyter = ["jupyterlab>=4.3.6"]
+r = ["anndata2ri>=1.3", "rpy2>=3.5"]
+scanpy = ["scanpy[leiden,skmisc]>=1.10"]
+test = ["pytest>=8.3.4"]
 
 [build-system]
 requires = ["flit_core>=3.2,<4"]
@@ -65,4 +67,5 @@ dev = [
     "scanpy[harmony,leiden,scrublet,skmisc]>=1.10.4",
     "jupyterlab>=4.3.6",
     "sclab-tools",
+    "scrublet>=0.2.3",
 ]

{sclab-0.2.5 → sclab-0.3.0}/src/sclab/__init__.py

@@ -6,4 +6,4 @@ __all__ = [
     "SCLabDashboard",
 ]
 
-__version__ = "0.2.5"
+__version__ = "0.3.0"

{sclab-0.2.5 → sclab-0.3.0}/src/sclab/dataset/_dataset.py

@@ -365,7 +365,7 @@ class SCLabDataset(EventClient):
         if not index.isin(self.metadata.index).all():
             raise InvalidRowSubset("index contains invalid values")
 
-        self.adata = self.adata[index].copy()
+        self.adata._inplace_subset_obs(index)
 
         self.broker.publish("dset_total_rows_change", self.metadata)
 

{sclab-0.2.5 → sclab-0.3.0}/src/sclab/examples/processor_steps/__init__.py

@@ -1,5 +1,6 @@
 from ._cluster import Cluster
 from ._differential_expression import DifferentialExpression
+from ._doublet_detection import DoubletDetection
 from ._gene_expression import GeneExpression
 from ._integration import Integration
 from ._neighbors import Neighbors
@@ -16,6 +17,7 @@ __all__ = [
     "Neighbors",
     "UMAP",
     "Cluster",
+    "DoubletDetection",
     "GeneExpression",
     "DifferentialExpression",
 ]

sclab-0.3.0/src/sclab/examples/processor_steps/_doublet_detection.py

@@ -0,0 +1,68 @@
+from ipywidgets import Dropdown
+
+from sclab.dataset.processor import Processor
+from sclab.dataset.processor.step import ProcessorStepBase
+from sclab.tools.doublet_detection import scrublet
+
+# from sclab.tools.doublet_detection import doubletdetection
+# from sclab.tools.doublet_detection import scdblfinder
+
+
+class DoubletDetection(ProcessorStepBase):
+    parent: Processor
+    name: str = "doublet_detection"
+    description: str = "Doublet Detection"
+
+    def __init__(self, parent: Processor) -> None:
+        variable_controls = dict(
+            layer=Dropdown(
+                options=tuple(parent.dataset.adata.layers.keys()),
+                value=None,
+                description="Layer",
+            ),
+            flavor=Dropdown(
+                options=[
+                    "scrublet",
+                    # "doubletdetection",
+                    # "scDblFinder",
+                ],
+                description="Flavor",
+            ),
+        )
+
+        super().__init__(
+            parent=parent,
+            fixed_params={},
+            variable_controls=variable_controls,
+        )
+
+    def function(self, layer: str, flavor: str):
+        adata = self.parent.dataset.adata
+
+        kvargs = {"adata": adata, "layer": layer, "key_added": flavor}
+
+        self.broker.std_output.clear_output(wait=False)
+        with self.broker.std_output:
+            match flavor:
+                # case "scDblFinder":
+                #     scdblfinder(**kvargs, clusters_col="leiden")
+
+                # case "doubletdetection":
+                #     doubletdetection(
+                #         **kvargs,
+                #         pseudocount=1,
+                #         clustering_algorithm="leiden",
+                #         clustering_kwargs=dict(resolution=5.0),
+                #     )
+
+                case "scrublet":
+                    scrublet(**kvargs)
+
+                case _:
+                    raise ValueError(f"Unknown flavor: {flavor}")
+
+        self.broker.publish(
+            "dset_metadata_change",
+            self.parent.dataset.metadata,
+            f"{flavor}_label",
+        )

{sclab-0.2.5 → sclab-0.3.0}/src/sclab/examples/processor_steps/_integration.py

@@ -1,4 +1,4 @@
-from ipywidgets import Dropdown
+from ipywidgets import Dropdown, IntText
 
 from sclab.dataset.processor import Processor
 from sclab.dataset.processor.step import ProcessorStepBase
@@ -40,20 +40,49 @@ class Integration(ProcessorStepBase):
                 value="batch" if "batch" in cat_options else None,
                 description="GroupBy",
             ),
+            reference_batch=Dropdown(
+                description="Reference Batch",
+            ),
             flavor=Dropdown(
                 options=["harmony", "scanorama"],
                 value="harmony",
                 description="Flavor",
             ),
+            max_iters=IntText(
+                value=20,
+                description="Max iters",
+            ),
         )
 
+        def update_reference_batch(*args, **kwargs):
+            group_by = variable_controls["group_by"].value
+            options = {
+                "": None,
+                **{
+                    c: c
+                    for c in self.parent.dataset.adata.obs[group_by]
+                    .sort_values()
+                    .unique()
+                },
+            }
+            variable_controls["reference_batch"].options = options
+
+        variable_controls["group_by"].observe(update_reference_batch, names="value")
+
         super().__init__(
             parent=parent,
             fixed_params={},
             variable_controls=variable_controls,
         )
 
-    def function(self, use_rep: str, group_by: str, flavor: str):
+    def function(
+        self,
+        use_rep: str,
+        group_by: str,
+        flavor: str,
+        reference_batch: str | None,
+        max_iters: int,
+    ):
         adata = self.parent.dataset.adata
 
         key_added = f"{use_rep}_{flavor}"
@@ -68,9 +97,13 @@ class Integration(ProcessorStepBase):
         with self.broker.std_output:
             match flavor:
                 case "harmony":
-                    from scanpy.external.pp import harmony_integrate
+                    from sclab.preprocess import harmony_integrate
 
-                    harmony_integrate(**kvargs)
+                    harmony_integrate(
+                        **kvargs,
+                        reference_batch=reference_batch,
+                        max_iter_harmony=max_iters,
+                    )
 
                 case "scanorama":
                     from scanpy.external.pp import scanorama_integrate

{sclab-0.2.5 → sclab-0.3.0}/src/sclab/examples/processor_steps/_neighbors.py

@@ -1,4 +1,4 @@
-from ipywidgets import Dropdown, IntText
+from ipywidgets import Dropdown, IntRangeSlider, IntText
 
 from sclab.dataset.processor import Processor
 from sclab.dataset.processor.step import ProcessorStepBase
@@ -22,7 +22,12 @@ class Neighbors(ProcessorStepBase):
                 description="Use rep.",
             ),
             n_neighbors=IntText(value=20, description="N neighbors"),
-            n_dims=IntText(value=10, description="N Dims"),
+            dims=IntRangeSlider(
+                min=1,
+                max=30,
+                value=(1, 10),
+                description="Use dims",
+            ),
             metric=Dropdown(
                 options=["euclidean", "cosine"],
                 value="euclidean",
@@ -31,6 +36,14 @@ class Neighbors(ProcessorStepBase):
             **parent.make_groupbybatch_checkbox(),
         )
 
+        def update_dims_range(*args, **kwargs):
+            adata = self.parent.dataset.adata
+            use_rep = variable_controls["use_rep"].value
+            max_dim = adata.obsm[use_rep].shape[1]
+            variable_controls["dims"].max = max_dim
+
+        variable_controls["use_rep"].observe(update_dims_range, names="value")
+
         super().__init__(
             parent=parent,
             fixed_params={},
@@ -41,13 +54,20 @@ class Neighbors(ProcessorStepBase):
         self,
         n_neighbors: int = 20,
         use_rep: str = "X_pca",
-        n_dims: int = 10,
+        dims: tuple[int, int] = (1, 10),
         metric: str = "euclidean",
         group_by_batch: bool = False,
     ):
         import scanpy as sc
 
         adata = self.parent.dataset.adata
+        min_dim, max_dim = dims
+        min_dim = min_dim - 1
+
+        if min_dim > 0:
+            adata.obsm[use_rep + "_trimmed"] = adata.obsm[use_rep][:, min_dim:max_dim]
+            use_rep = use_rep + "_trimmed"
+        n_dims = max_dim - min_dim
 
         if group_by_batch and self.parent.batch_key:
             group_by = self.parent.batch_key
@@ -58,7 +78,7 @@ class Neighbors(ProcessorStepBase):
                 n_pcs=n_dims,
                 use_annoy=False,
                 metric=metric,
-                pynndescent_n_neighbors=n_neighbors,
+                neighbors_within_batch=n_neighbors,
             )
         else:
             sc.pp.neighbors(

{sclab-0.2.5 → sclab-0.3.0}/src/sclab/examples/processor_steps/_pca.py

@@ -1,4 +1,3 @@
-import numpy as np
 import pandas as pd
 import plotly.express as px
 from ipywidgets import Button, Dropdown, IntText
@@ -64,7 +63,9 @@ class PCA(ProcessorStepBase):
         counts_layer = self.parent.dataset.counts_layer
 
         if reference_batch:
-            obs_mask = adata.obs[self.parent.batch_key] == reference_batch
+            batch_key = self.parent.batch_key
+
+            obs_mask = adata.obs[batch_key] == reference_batch
             adata_ref = adata[obs_mask].copy()
             if mask_var == "highly_variable":
                 sc.pp.highly_variable_genes(
@@ -85,13 +86,12 @@ class PCA(ProcessorStepBase):
             uns_pca = adata_ref.uns["pca"]
             uns_pca["reference_batch"] = reference_batch
             PCs = adata_ref.varm["PCs"]
-            X_pca: np.ndarray = adata.X.dot(PCs)
-            X_pca = X_pca - X_pca.mean(axis=0, keepdims=True)
-            adata.obsm["X_pca"] = X_pca
+            adata.obsm["X_pca"] = adata.X.dot(PCs)
             adata.uns["pca"] = uns_pca
             adata.varm["PCs"] = PCs
         else:
             sc.pp.pca(adata, n_comps=n_comps, mask_var=mask_var, svd_solver="arpack")
+            adata.obsm["X_pca"] = adata.X.dot(adata.varm["PCs"])
 
         self.plot_variance_ratio_button.disabled = False
         self.broker.publish(

{sclab-0.2.5 → sclab-0.3.0}/src/sclab/examples/processor_steps/_preprocess.py

@@ -1,4 +1,7 @@
+import warnings
+
 import numpy as np
+from anndata import ImplicitModificationWarning
 from ipywidgets import Checkbox, Dropdown
 from tqdm.auto import tqdm
 
@@ -156,7 +159,17 @@ class Preprocess(ProcessorStepBase):
 
         if scale:
             new_layer += "_scale"
-            sc.pp.scale(adata, zero_center=False)
+            if group_by is not None:
+                for _, idx in adata.obs.groupby(group_by, observed=True).groups.items():
+                    with warnings.catch_warnings():
+                        warnings.filterwarnings(
+                            "ignore",
+                            category=ImplicitModificationWarning,
+                            message="Modifying `X` on a view results in data being overridden",
+                        )
+                        adata[idx].X = sc.pp.scale(adata[idx].X, zero_center=False)
+            else:
+                sc.pp.scale(adata, zero_center=False)
 
         adata.layers[new_layer] = adata.X.copy()
 

{sclab-0.2.5 → sclab-0.3.0}/src/sclab/examples/processor_steps/_qc.py

@@ -1,3 +1,4 @@
+import numpy as np
 from ipywidgets import Dropdown, IntText
 
 from sclab.dataset.processor import Processor
@@ -21,6 +22,7 @@ class QC(ProcessorStepBase):
                 value="counts",
                 description="Layer",
             ),
+            min_counts=IntText(value=50, description="Min. Counts"),
             min_genes=IntText(value=5, description="Min. Genes"),
             min_cells=IntText(value=0, description="Min. Cells"),
             max_rank=IntText(value=0, description="Max. Rank"),
@@ -45,8 +47,10 @@ class QC(ProcessorStepBase):
     def compute_qc_metrics(
         self,
         layer: str | None = None,
+        min_counts: int = 50,
         min_genes: int = 5,
         min_cells: int = 5,
+        max_rank: int = 0,
     ):
         import scanpy as sc
 
@@ -58,6 +62,11 @@ class QC(ProcessorStepBase):
 
         adata.layers["qc_tmp_current_X"] = adata.X
         adata.X = adata.layers[layer].copy()
+        rowsums = np.asarray(adata.X.sum(axis=1)).squeeze()
+
+        obs_idx = adata.obs_names[rowsums >= min_counts]
+        adata._inplace_subset_obs(obs_idx)
+
         sc.pp.calculate_qc_metrics(adata, percent_top=None, log1p=False, inplace=True)
 
         sc.pp.filter_cells(adata, min_genes=min_genes)
@@ -68,19 +77,26 @@ class QC(ProcessorStepBase):
         # Restore original X
         adata.X = adata.layers.pop("qc_tmp_current_X")
 
+        if max_rank > 0:
+            series = self.parent.dataset.adata.obs["barcode_rank"]
+            index = series.loc[series < max_rank].index
+            self.parent.dataset.filter_rows(index)
+
     def function(
         self,
         layer: str | None = None,
+        min_counts: int = 50,
         min_genes: int = 5,
         min_cells: int = 5,
         max_rank: int = 0,
     ):
-        self.compute_qc_metrics(layer, min_genes, min_cells)
-
-        if max_rank > 0:
-            series = self.parent.dataset.adata.obs["barcode_rank"]
-            index = series.loc[series < max_rank].index
-            self.parent.dataset.filter_rows(index)
+        self.compute_qc_metrics(
+            layer,
+            min_counts,
+            min_genes,
+            min_cells,
+            max_rank,
+        )
 
         self.broker.publish("dset_metadata_change", self.parent.dataset.metadata)
         self.broker.publish(

sclab-0.3.0/src/sclab/gui/components/__init__.py

@@ -0,0 +1,5 @@
+from ._guided_pseudotime import GuidedPseudotime
+
+__all__ = [
+    "GuidedPseudotime",
+]