add datamodule for demo

setup.py

@@ -2,7 +2,7 @@
 __module_name__ = "setup.py"
 __doc__ = """PYPI package distribution setup."""
 __author__ = ", ".join(["Michael E. Vinyard"])
-__email__ = ", ".join(["[email protected]"])
+__email__ = ", ".join(["[email protected]"])
 
 
 # -- import packages: ----------------------------------------------------------
@@ -15,10 +15,10 @@
 # -- run setup: ----------------------------------------------------------------
 setuptools.setup(
     name="torch-adata",
-    version="0.0.23",
+    version="0.0.24rc0",
     python_requires=">3.9.0",
     author="Michael E. Vinyard",
-    author_email="mvinyard@g.harvard.edu",
+    author_email="mvinyard[email protected]",
     url=None,
     long_description=open("README.md", encoding="utf-8").read(),
     long_description_content_type="text/markdown",
@@ -28,11 +28,15 @@
         "anndata>=0.9.1",
         "licorice_font>=0.0.3",
         "lightning>=2.0.1",
-        "torch>=2.0",        
+        "torch>=2.0",
+        "numpy==1.24",
+        "scanpy==1.9.3",
+        "scikit-learn==1.2.2",
+        "webfiles",
     ],
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
-        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.9",
         "Intended Audience :: Science/Research",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],

torch_adata/_demo/__init__.py

@@ -1,2 +1,5 @@
 
-from ._plot_umap import PlotUMAP
+from ._plot_umap import PlotUMAP
+from ._pbmc_3k import PBMC3k
+from ._larry import LARRY
+from ._demo_data import DemoData

torch_adata/_demo/_demo_data.py

@@ -0,0 +1,26 @@
+
+
+from .. import _utils as utils
+from ._pbmc_3k import PBMC3k
+from ._larry import LARRY
+
+
+class DemoData(utils.ABCParse):
+    def __init__(self):
+        """"""
+
+    @property
+    def PBMC3k(self):
+        if not hasattr(self, "_pbmcs"):
+            self._pbmcs = PBMC3k()
+        else:
+            self._pbmcs.plot()
+        return self._pbmcs.adata
+
+    @property
+    def LARRY(self):
+        if not hasattr(self, "_larry"):
+            self._larry = LARRY()
+        else:
+            self._larry.plot()
+        return self._larry.adata

torch_adata/_demo/_larry.py

@@ -0,0 +1,56 @@
+
+import vinplots
+import anndata
+import os
+import web_files
+
+from .. import _utils as utils
+from ._plot_umap import PlotUMAP
+
+class LARRY(utils.ABCParse):
+    _HTTP_ADDRESS = "https://figshare.com/ndownloader/files/38171943"
+
+    def __init__(self, filename="adata.LARRY.h5ad", data_dir="data", silent=False):
+        self._config(locals())
+
+    def _config(self, kwargs):
+        """"""
+
+        self.__parse__(kwargs, public=[None])
+
+        self._INFO = utils.InfoMessage()
+
+        if not os.path.exists(self._data_dir):
+            os.mkdir(self._data_dir)
+
+    def _download(self):
+        msg = "Downloading {:.<10}...".format(self._filename)
+        self._INFO(msg, end=" ")
+        f = web_files.WebFile(
+            http_address=self._HTTP_ADDRESS,
+            local_path=self.local_path,
+        )
+        f.download()
+        print("Done.")
+
+    @property
+    def local_path(self):
+        return os.path.join(self._data_dir, self._filename)
+
+    @property
+    def adata(self):
+        if not hasattr(self, "_adata"):
+            if not os.path.exists(self.local_path):
+                self._download()
+            self._adata = anndata.read_h5ad(self.local_path)
+            self._adata.uns["cmap"] = vinplots.colors.LARRY_in_vitro
+            if not self._silent:
+                print(self._adata)
+                self.plot()
+        return self._adata
+
+    def plot(self):
+        umap_plot = PlotUMAP(
+            self._adata, title="LARRY hematopoiesis"
+        )
+        umap_plot(groupby="Cell type annotation")

torch_adata/_demo/_pbmc_3k.py

@@ -0,0 +1,39 @@
+
+# -- import packages: --------------------------------------------------------
+import scanpy as sc
+import pandas as pd
+import vinplots
+
+
+from .. import _utils as utils
+from ._plot_umap import PlotUMAP
+
+class PBMC3k(utils.ABCParse):
+    def __init__(self, silent=False):
+        self.__parse__(locals(), public=[None])
+
+    def _configure(self):
+        _adata = sc.datasets.pbmc3k_processed()
+        cell_type_df = pd.DataFrame(_adata.obs["louvain"].unique()).reset_index()
+        cell_type_df.columns = ["cell_type_idx", "louvain"]
+        df_obs = _adata.obs.merge(cell_type_df, on="louvain", how="left")
+        df_obs.index = df_obs.index.astype(str)
+        _adata.obs = df_obs
+        _adata.uns["cmap"] = vinplots.colors.pbmc3k
+        return _adata
+
+    @property
+    def adata(self):
+        if not hasattr(self, "_adata"):
+            self._adata = self._configure()
+            if not self._silent:
+                print(self._adata)
+                self.plot()
+        return self._adata
+
+    def plot(self):
+        umap_plot = PlotUMAP(
+            self._adata, title="10x PBMCs (~3k cells)"
+        )
+        umap_plot(groupby="louvain")
+

torch_adata/_demo/_plot_umap.py

@@ -31,14 +31,19 @@ def CMAP(self):
         return self.adata.uns[self._cmap_key]
 
     def _plot_grouped(self):
-        for group, group_df in self.adata.obs.groupby(self.groupby):
+        for en, (group, group_df) in enumerate(self.adata.obs.groupby(self.groupby)):
+            if group in self.plot_behind:
+                z = 0
+            else:
+                z = en + 1
             xu = self.adata[group_df.index].obsm[self._use_key]
             self.axes[0].scatter(
                 xu[:, 0],
                 xu[:, 1],
                 label=group,
                 color=self.CMAP[group],
                 alpha=self._alpha,
+                zorder = z,
             )
 
     def _format(self):
@@ -51,6 +56,7 @@ def _format(self):
     def __call__(
         self,
         groupby=None,
+        plot_behind = ["Undifferentiated"],
     ):
         self.__update__(locals())
 

torch_adata/_utils/_info_message.py

@@ -7,7 +7,7 @@ def __init__(self, INFO="INFO", color="BLUE"):
     def _format_msg_title(self, INFO):
         return f" - [{INFO}] | "
 
-    def __call__(self, msg):
+    def __call__(self, msg, end = "\n"):
 
         self.BASE = self._format_msg_title(self.INFO)
-        print(self.BASE + msg)
+        print(self.BASE + msg, end = end)