adding new function napariGater

labsyspharm · Nov 20, 2024 · 44f4437 · 44f4437
1 parent 7082470
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Showing 9 changed files with 468 additions and 6 deletions.
diff --git a/docs/Functions/pl/napariGater.md b/docs/Functions/pl/napariGater.md
@@ -0,0 +1,5 @@
+---
+hide:
+  - toc        # Hide table of contents
+---
+::: scimap.plotting.napariGater
diff --git a/docs/Tools Shortcut.md b/docs/Tools Shortcut.md
@@ -51,6 +51,7 @@ import scimap as sm
 | [`sm.pl.image_viewer`](Functions/pl/image_viewer.md) | Integrates with `napari` to offer an interactive platform for enhanced image viewing and annotation with data overlays. |
 | [`sm.pl.addROI_image`](Functions/pl/addROI_image.md) | Facilitates the addition of Regions of Interest (ROIs) through `napari`, enriching spatial analyses with precise locational data. |
 | [`sm.pl.gate_finder`](Functions/pl/gate_finder.md) | Aids in the manual gating process by overlaying marker positivity on images, simplifying the identification and analysis of cellular subsets. |
+| [`sm.pl.napariGater`](Functions/pl/napariGater.md) | Modified version of gate_finder and soon to replace it. |
 | [`sm.pl.heatmap`](Functions/pl/heatmap.md) | Creates heatmaps to visually explore marker expression or feature distributions across different groups. |
 | [`sm.pl.markerCorrelation`](Functions/pl/markerCorrelation.md) | Computes and visualizes the correlation among selected markers. |
 | [`sm.pl.groupCorrelation`](Functions/pl/groupCorrelation.md) | Calculates and displays the correlation between the abundances of groups across user defined conditions. |

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 
 name = "SCIMAP"
-version = "2.1.3"
+version = "2.2.0"
 description = "Spatial Single-Cell Analysis Toolkit"
 
 license = "MIT"

diff --git a/scimap/plotting/__init__.py b/scimap/plotting/__init__.py
@@ -16,4 +16,5 @@
 from .heatmap import heatmap
 from .markerCorrelation import markerCorrelation
 from .groupCorrelation import groupCorrelation
-from .spatialInteractionNetwork import spatialInteractionNetwork
+from .spatialInteractionNetwork import spatialInteractionNetwork
+from .napariGater import napariGater
diff --git a/scimap/plotting/gate_finder.py b/scimap/plotting/gate_finder.py
@@ -13,6 +13,15 @@
 ## Function
 """
 
+import warnings
+
+warnings.warn(
+    "gate_finder() is deprecated and will be removed in a future version. "
+    "Please use sm.pl.napariGater() instead.",
+    FutureWarning,
+    stacklevel=2,
+)
+
 try:
     import napari
 except: