Testing minor fixes

napari_spacetx_explorer/__init__.py

@@ -1,11 +1,11 @@
 try:
     from ._version import version as __version__
 except ImportError:
-    __version__ = "0.1.4"
+    __version__ = "0.1.5"
 
 
 from ._reader import napari_get_reader
-from ._function import napari_experimental_provide_function
+from ._function2 import napari_experimental_provide_function
 #from ._dock_widget import napari_experimental_provide_dock_widget
 #from ._summary import napari_experimental_provide_function
 #from ._function import napari_experimental_provide_function

napari_spacetx_explorer/_function2.py

@@ -0,0 +1,64 @@
+from typing import TYPE_CHECKING
+from enum import Enum
+import numpy as np
+from napari_plugin_engine import napari_hook_implementation
+if TYPE_CHECKING:
+    import napari
+
+@napari_hook_implementation
+def napari_experimental_provide_function():
+    return read_spots
+
+def read_spots(
+        points: "napari.layers.Points",
+        genes: str = 'IGHG1',
+        color_s: str = 'white',
+        size_s: str = '10'
+) -> "napari.types.LayerDataTuple":
+    """Retrieve points' data from selected group of genes.
+
+    Parameters
+    ----------
+    points: napari.types.PointsData
+        The raw data from a decoded CSV file
+    genes: list
+        list with genes to visualize.
+
+    Returns
+    -------
+    layer_data: napari.types.LayerDataTuple
+        The layer data tuple containing the corresponding
+        points and metadata for visualization.
+    """
+    genes_list = genes.split(',')
+    genes_dict_cmap = {g: i for i, g in enumerate(genes_list)}
+
+    color_cycle = color_s.split(',')
+    size_cycle = [int(i) for i in size_s.split(',')]
+
+    spots_idx = [genes_dict_cmap[g] for g in points.properties['gene'] if g in genes_list]
+
+    # List with indices of selected genes by user.
+    selected_points_idx = [i for i in range(len(points.data)) if points.properties['gene'][i] in genes_list]
+
+    # Here we select the data coordinates and labels/index of requested genes:
+    selected_data = [points.data[i] for i in selected_points_idx]
+    spot_properties = {'label': spots_idx}
+
+    face_color = {
+        'colors': 'label',
+        'color_mode': 'cycle',
+        'categorical_colormap': color_cycle
+    }
+
+    layer_data = (
+        selected_data,
+        #{'face_color': 'magenta',
+        # 'symbol': 'ring'},
+        {'properties': spot_properties,
+         'size': size_cycle,
+         'face_color': face_color},
+        'Points'
+    )
+
+    return [layer_data]

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napari-spacetx-explorer
-version = 0.1.4
+version = 0.1.5
 author = Sebastian Gonzalez-Tirado
 author_email = sebgoti8@gmail.com
 license = BSD-3-Clause