sclab 0.2.2__py3-none-any.whl → 0.2.4__py3-none-any.whl

sclab/__init__.py

@@ -6,4 +6,4 @@ __all__ = [
     "SCLabDashboard",
 ]
 
-__version__ = "0.2.2"
+__version__ = "0.2.4"

sclab/_io.py

@@ -58,12 +58,6 @@ def load_adata_from_url(
     assert is_valid_url(url), "URL is not valid"
     url_path = Path(urlparse(url).path)
 
-    if url_path.suffix == ".h5":
-        try:
-            import scanpy as sc
-        except ImportError:
-            raise ImportError("Please install scanpy: `pip install scanpy`")
-
     file_content = fetch_file(url, progress=progress)
     match url_path.suffix:
         case ".h5":

sclab/_sclab.py

@@ -187,7 +187,7 @@ class DataLoader(VBox):
         user_f_locals = inspect.stack()[2].frame.f_locals
         self.defined_adatas_dict = {}
         for name, variable_type in [(k, type(v)) for k, v in user_f_locals.items()]:
-            if variable_type is AnnData:
+            if variable_type is AnnData and not name.startswith("_"):
                 self.defined_adatas_dict[name] = user_f_locals[name]
 
         self.defined_adatas_label = Label(

sclab/examples/processor_steps/__init__.py

@@ -1,5 +1,7 @@
 from ._cluster import Cluster
 from ._differential_expression import DifferentialExpression
+from ._gene_expression import GeneExpression
+from ._integration import Integration
 from ._neighbors import Neighbors
 from ._pca import PCA
 from ._preprocess import Preprocess
@@ -10,8 +12,10 @@ __all__ = [
     "QC",
     "Preprocess",
     "PCA",
+    "Integration",
     "Neighbors",
     "UMAP",
     "Cluster",
+    "GeneExpression",
     "DifferentialExpression",
 ]

sclab/examples/processor_steps/_gene_expression.py

@@ -0,0 +1,125 @@
+import numpy as np
+import pandas as pd
+import plotly.colors as pc
+import plotly.express as px
+from ipywidgets import Combobox, Dropdown
+
+from sclab.dataset.processor import Processor
+from sclab.dataset.processor.step import ProcessorStepBase
+
+colorscales = list(
+    filter(lambda s: "swatch" not in s and not s.startswith("_"), dir(pc.sequential))
+)
+
+
+class GeneExpression(ProcessorStepBase):
+    parent: Processor
+    name: str = "gene_expression"
+    description: str = "Gene Expression"
+
+    run_button_description = "Plot Expression"
+
+    def __init__(self, parent: Processor) -> None:
+        df = parent.dataset.metadata.select_dtypes("number")
+        df = parent.dataset.metadata
+        axis_key_options = {"": None, **{c: c for c in df.columns}}
+
+        gene_input_options = parent.dataset.adata.var_names
+        genes_df = parent.dataset.adata.var
+        info_cols = ["name", "symbol", "description"]
+        for col in [
+            c for c in genes_df.columns if any([s.lower() in c for s in info_cols])
+        ]:
+            new_info = genes_df[col].astype(str).str.replace("nan", "")
+            gene_input_options = gene_input_options + " - " + new_info
+
+        variable_controls = dict(
+            gene_input=Combobox(
+                placeholder="Type gene name",
+                options=gene_input_options.to_list(),
+                description="Gene",
+                ensure_option=True,
+            ),
+            layer=Dropdown(
+                options=tuple(parent.dataset.adata.layers.keys()),
+                value=None,
+                description="Layer",
+            ),
+            time_key=Dropdown(
+                options=axis_key_options,
+                value=None,
+                description="Horiz. axis",
+            ),
+            colorscale=Dropdown(
+                options=colorscales, value="Oryel", description="Col. scale"
+            ),
+        )
+
+        super().__init__(
+            parent=parent,
+            fixed_params={},
+            variable_controls=variable_controls,
+        )
+
+        self.variable_controls["gene_input"].observe(self.send_plot, names="value")
+        self.variable_controls["layer"].observe(self.send_plot, names="value")
+        self.variable_controls["time_key"].observe(self.send_plot, names="value")
+        self.variable_controls["colorscale"].observe(self.send_plot, names="value")
+
+    def function(self, *pargs, **kwargs):
+        self.send_plot({})
+
+    def send_plot(self, change: dict):
+        adata = self.parent.dataset.adata
+        metadata = self.parent.dataset.metadata
+        selected_cells = self.parent.dataset.selected_rows
+
+        gene_input: str = self.variable_controls["gene_input"].value
+        layer: str = self.variable_controls["layer"].value
+        time_key: str = self.variable_controls["time_key"].value
+        colorscale: str = self.variable_controls["colorscale"].value
+
+        if gene_input is None or gene_input == "":
+            self.update_output("")
+            return
+
+        if layer is None or layer == "":
+            self.update_output("")
+            return
+
+        gene_id = gene_input.split(" ")[0]
+
+        if layer == "X":
+            X = adata[:, gene_id].X
+        else:
+            X = adata[:, gene_id].layers[layer]
+
+        E = np.asarray(X.sum(axis=1)).flatten()
+
+        self.update_output(f"Showing gene: {gene_id}")
+        # self.variable_controls["gene_input"].value = ""
+
+        df = pd.DataFrame({gene_id: E}, index=adata.obs.index)
+        metadata = metadata.join(df)
+        if selected_cells.size > 0:
+            metadata = metadata.loc[selected_cells]
+
+        if time_key is None:
+            self.broker.publish(
+                "dplt_plot_figure_request",
+                metadata=metadata,
+                colorby=gene_id,
+                color_continuous_scale=colorscale,
+            )
+            return
+
+        fig = px.scatter(
+            metadata,
+            x=time_key,
+            y=gene_id,
+            color=gene_id,
+            color_continuous_scale=colorscale,
+            hover_name=adata.obs.index,
+            title=f"Gene: {gene_id}, Layer: {layer}",
+        )
+        self.broker.publish("dplt_plot_figure_request", figure=fig)

sclab/examples/processor_steps/_integration.py

@@ -0,0 +1,86 @@
+from ipywidgets import Dropdown
+
+from sclab.dataset.processor import Processor
+from sclab.dataset.processor.step import ProcessorStepBase
+
+
+class Integration(ProcessorStepBase):
+    parent: Processor
+    name: str = "integration"
+    description: str = "Integration"
+
+    def __init__(self, parent: Processor) -> None:
+        try:
+            from scanpy.external.pp import harmony_integrate  # noqa
+        except ImportError:
+            try:
+                from scanpy.external.pp import scanorama_integrate  # noqa
+            except ImportError:
+                raise ImportError(
+                    "Integration requires scanorama or harmony to be installed.\n"
+                    "\nInstall with one of:\n"
+                    "\npip install harmony"
+                    "\npip install scanorama"
+                    "\n"
+                )
+
+        cat_metadata = parent.dataset._metadata.select_dtypes(
+            include=["object", "category"]
+        )
+        cat_options = {"": None, **{c: c for c in cat_metadata.columns}}
+
+        variable_controls = dict(
+            use_rep=Dropdown(
+                options=tuple(parent.dataset.adata.obsm.keys()),
+                value=None,
+                description="Use rep.",
+            ),
+            group_by=Dropdown(
+                options=cat_options,
+                value="batch" if "batch" in cat_options else None,
+                description="GroupBy",
+            ),
+            flavor=Dropdown(
+                options=["harmony", "scanorama"],
+                value="harmony",
+                description="Flavor",
+            ),
+        )
+
+        super().__init__(
+            parent=parent,
+            fixed_params={},
+            variable_controls=variable_controls,
+        )
+
+    def function(self, use_rep: str, group_by: str, flavor: str):
+        adata = self.parent.dataset.adata
+
+        key_added = f"{use_rep}_{flavor}"
+        kvargs = {
+            "adata": adata,
+            "key": group_by,
+            "basis": use_rep,
+            "adjusted_basis": key_added,
+        }
+
+        self.broker.std_output.clear_output(wait=False)
+        with self.broker.std_output:
+            match flavor:
+                case "harmony":
+                    from scanpy.external.pp import harmony_integrate
+
+                    harmony_integrate(**kvargs)
+
+                case "scanorama":
+                    from scanpy.external.pp import scanorama_integrate
+
+                    scanorama_integrate(**kvargs)
+                case _:
+                    raise ValueError(f"Unknown flavor: {flavor}")
+
+        self.broker.publish(
+            "dset_data_dict_change",
+            self.parent.dataset.data_dict,
+            key_added,
+        )

sclab/examples/processor_steps/_preprocess.py

@@ -129,7 +129,6 @@ class Preprocess(ProcessorStepBase):
         if normalize_total:
             new_layer += "_normt"
             sc.pp.normalize_total(adata, target_sum=1e4)
-            adata.layers[new_layer] = adata.X.copy()
 
         pbar.update(10)
         pbar.update(10)
@@ -138,7 +137,6 @@ class Preprocess(ProcessorStepBase):
             new_layer += "_log1p"
             adata.uns.pop("log1p", None)
             sc.pp.log1p(adata)
-            adata.layers[new_layer] = adata.X.copy()
         pbar.update(10)
 
         vars_to_regress = []
@@ -154,13 +152,13 @@ class Preprocess(ProcessorStepBase):
         if vars_to_regress:
             new_layer += "_regr"
             sc.pp.regress_out(adata, keys=vars_to_regress, n_jobs=1)
-            adata.layers[new_layer] = adata.X.copy()
         pbar.update(10)
 
         if scale:
             new_layer += "_scale"
             sc.pp.scale(adata, zero_center=False)
-            adata.layers[new_layer] = adata.X.copy()
+
+        adata.layers[new_layer] = adata.X.copy()
 
         pbar.update(10)
 

sclab/methods/__init__.py

@@ -5,6 +5,8 @@ from ..examples.processor_steps import (
     UMAP,
     Cluster,
     DifferentialExpression,
+    GeneExpression,
+    Integration,
     Neighbors,
     Preprocess,
 )
@@ -13,16 +15,20 @@ __all__ = [
     "QC",
     "Preprocess",
     "PCA",
+    "Integration",
     "Neighbors",
     "UMAP",
     "Cluster",
+    "GeneExpression",
     "DifferentialExpression",
 ]
 
 register_sclab_method("Processing")(QC)
 register_sclab_method("Processing")(Preprocess)
 register_sclab_method("Processing")(PCA)
+register_sclab_method("Processing")(Integration)
 register_sclab_method("Processing")(Neighbors)
 register_sclab_method("Processing")(UMAP)
 register_sclab_method("Processing")(Cluster)
+register_sclab_method("Analysis")(GeneExpression)
 register_sclab_method("Analysis")(DifferentialExpression)

{sclab-0.2.2.dist-info → sclab-0.2.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sclab
-Version: 0.2.2
+Version: 0.2.4
 Summary: sclab
 Author-email: Argenis Arriojas <ArriojasMaldonado001@umb.edu>
 Requires-Python: >=3.10,<3.13
@@ -18,10 +18,10 @@ Requires-Dist: itables
 Requires-Dist: numpy<2.2
 Requires-Dist: pandas
 Requires-Dist: plotly<6.0
-Requires-Dist: requests>=2.32.3
+Requires-Dist: requests
 Requires-Dist: scikit-learn
 Requires-Dist: svgpathtools
-Requires-Dist: tqdm>=4.67.1
+Requires-Dist: tqdm
 Requires-Dist: jupyterlab>=4.3.6 ; extra == "jupyter"
 Requires-Dist: scanpy[leiden, skmisc]>=1.10 ; extra == "scanpy"
 Requires-Dist: pytest>=8.3.4 ; extra == "test"

{sclab-0.2.2.dist-info → sclab-0.2.4.dist-info}/RECORD

@@ -1,7 +1,7 @@
-sclab/__init__.py,sha256=UaTIrqZIaNx_mwX7RPdk93mDBq1fkZaElCiMA-bvBIM,132
-sclab/_io.py,sha256=21EHrUvYV8WFRbBcdeuWXbApUIITHaXbqgDI8lqQgHo,2852
+sclab/__init__.py,sha256=0XdhioNKeydnAhDycQGD86UAWtEWc9IgYWY4PQKEWPE,132
+sclab/_io.py,sha256=5ISxIPbE233UiOt3QEs9fkLO8DLLEe5HrMnZoR-KLYE,2662
 sclab/_methods_registry.py,sha256=RcffyRuuLzHqsnAdbBL4W1GmZx80d9AxdGjUnx1mbNg,1704
-sclab/_sclab.py,sha256=Fq-GrhapzziTzJgkpPjdjYtjeQpBeXWYVUbPY6axg-A,8688
+sclab/_sclab.py,sha256=kgjChI0h9fVI3sg8O32CJp57KTmoRQ53jGt8eu-_hCQ,8717
 sclab/dataset/__init__.py,sha256=f9PoXIMAPnC3Var1ODr3mXkotW6u6NRPQvlgcWYXk54,143
 sclab/dataset/_dataset.py,sha256=dJeiEfo-f6eM866-d53H6FUF9IR-OK4vwDojSq_og0Q,14248
 sclab/dataset/_exceptions.py,sha256=g8RJL8PiRmD4--PkOs5CZth_qeaduvieMlKJNkrUIYA,45
@@ -20,15 +20,18 @@ sclab/event/_broker.py,sha256=W4GgoBhJS1LxGQv8TYFg71o5jUQPO8BDLrKzahDUyEM,7121
 sclab/event/_client.py,sha256=Kx7pza-CzLySR0JBBneiZQAjtllUnjWKNKSfw3K2ZQE,2362
 sclab/event/_utils.py,sha256=LehiFhn7dopNEaTFERJhs6fiVgXCBvseRxWTSWc6u-k,456
 sclab/examples/__init__.py,sha256=uSu4DMfF2K7xlZbLC_CmANyS3D56khGLMSVt6x9XXiI,68
-sclab/examples/processor_steps/__init__.py,sha256=KhbgN0-WrIhpgDZhWJOHr2Vxo0FB1ZBvM2bJK2Mjdmg,372
+sclab/examples/processor_steps/__init__.py,sha256=ymEOSOlQANfMcyjUQxFEzzzjoZFv8IejfnEFUfPqwKg,500
 sclab/examples/processor_steps/_cluster.py,sha256=olbri3HWPBU8p__r9kP9tgWaJoUJ2bK48pmHfdvf11c,1120
 sclab/examples/processor_steps/_differential_expression.py,sha256=uEToPiACCgo42oZidAw5DFgWVcDnChWzVRlVzn53K34,11567
+sclab/examples/processor_steps/_gene_expression.py,sha256=io_U53TQ3bpclGZ7xjuQHws4Lei5_nMpWTKbvD2zqs0,4216
+sclab/examples/processor_steps/_integration.py,sha256=Vzl2AdLJmnagPWtNYuqW-AmKbQ8jfRSKdui_DpQX1-8,2729
 sclab/examples/processor_steps/_neighbors.py,sha256=sEhLuuY-dCdwzqIarHpFVgM4tE1bW9Qa18xHOWA84Bk,2206
 sclab/examples/processor_steps/_pca.py,sha256=vit15FqHhWC-VSLSViduFt9V7dwakVvdnDOHxzJHiw0,4585
-sclab/examples/processor_steps/_preprocess.py,sha256=ffg8Vh-rSJPna08__xOlizu65QBBkRPinslnKRaRjbk,6336
+sclab/examples/processor_steps/_preprocess.py,sha256=pDPAzcqbHyX2zKrGY7HHNYCzrM-wI6VL7YGwUrkq9os,6172
 sclab/examples/processor_steps/_qc.py,sha256=KPWKxytu5YLXQ42uXe3ARKE36jqj5uidLhtyR-_TVBY,3238
 sclab/examples/processor_steps/_umap.py,sha256=Mzxj4LiZfh3WT5lS_BO_lTleC5jMoUm5_km_gvzU_I8,1402
-sclab/methods/__init__.py,sha256=FMxCemY8-TFHl-BUR6NNDUyOGAAGEhysIlXkSBQXV8g,646
+sclab/methods/__init__.py,sha256=gqqKIvai7E30IA5f4OnYZcyu5xUDF03GzYDkAZNhzr4,823
+sclab/scanpy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sclab/scanpy/_compat.py,sha256=VEdW4lWLtKmgLSrikRnfvYOz9EOa7e_iDt4Q88X9JKQ,2109
 sclab/scanpy/_settings.py,sha256=UVcJExVHsf_nvyZ5kTrBHPkddHCz7ARCzqAdZAM_A5E,16736
 sclab/scanpy/logging.py,sha256=VwSPeKjpXeopdcgEAlWDz2Wv4IGAAUv8GyMNpMART-0,8453
@@ -36,7 +39,7 @@ sclab/scanpy/readwrite.py,sha256=yixHonShUZ2Ms3Sv3UXw_VXlY00XDApvmyN2mZWFAcs,370
 sclab/scanpy/plotting/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sclab/scanpy/plotting/_rcmod.py,sha256=pc53dasHh2RFfTHVTbTb8v1z8vW032zjvum-WQLgjXA,1970
 sclab/scanpy/plotting/palettes.py,sha256=zHTM_CVfKazb32YreRx0-INllFssZP5rY_B7JTeaBhA,4782
-sclab-0.2.2.dist-info/licenses/LICENSE,sha256=LO7qldZoHIo9hc-HMBqclBh5800kZ9US9xTbLAQdHpg,1523
-sclab-0.2.2.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-sclab-0.2.2.dist-info/METADATA,sha256=GciGoDxIh9rPs3KVDs8EQqGq3fP_HfSxQxH4zBOuYVg,4289
-sclab-0.2.2.dist-info/RECORD,,
+sclab-0.2.4.dist-info/licenses/LICENSE,sha256=LO7qldZoHIo9hc-HMBqclBh5800kZ9US9xTbLAQdHpg,1523
+sclab-0.2.4.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+sclab-0.2.4.dist-info/METADATA,sha256=QwxGXc6enzoSEuRb1eEsNNzSn25PCgWk6EQK7hj6VRc,4273
+sclab-0.2.4.dist-info/RECORD,,