added to index

docs/Tools Shortcut.md

@@ -50,6 +50,7 @@ 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.heatmap`](Functions/pl/heatmap.md) | Creates heatmaps to visually explore marker expression or feature distributions across different groups. |
 | [`sm.pl.distPlot`](Functions/pl/distPlot.md) | Generates distribution plots for specific markers, allowing for the visual comparison of marker expression across different conditions or cell types. |
 | [`sm.pl.densityPlot2D`](Functions/pl/densityPlot2D.md) | Creates two-dimensional density plots of marker expressions, facilitating the visualization of expression patterns and densities in a spatial context. |
 | [`sm.pl.cluster_plots`](Functions/pl/cluster_plots.md) | Provides a meta-function that outputs a combination of UMAP, heatmap, and ranked markers for each group, offering a comprehensive view of clustering results. |

scimap/plotting/heatmap.py

@@ -102,13 +102,13 @@ def heatmap (adata,
         Returns a plot, if `saveDir` and `fileName` are provided, the plot is saved in the given directory.
 
 Example:
-    ```python
+        ```python
     
-    Example 1: Basic usage with clustering and standard scale by column.
+        # Example 1: Basic usage with clustering and standard scale by column.
     
         sm.pl.heatmap(adata, groupBy='leiden', standardScale='column')
     
-    Example 2: Advanced usage with specified subset markers, custom grouping, and file saving.
+        # Example 2: Advanced usage with specified subset markers, custom grouping, and file saving.
     
         subsetMarkers = ['ELANE', 'CD57', 'CD45', 'CD11B', 'SMA', 'CD16', 'ECAD']
         subsetGroups = ['0', '1', '3', '6']
@@ -119,7 +119,7 @@ def heatmap (adata,
         
         sm.pl.heatmap(adata, groupBy='leiden', subsetMarkers=subsetMarkers, subsetGroups=subsetGroups, clusterRows=False, clusterColumns=False, standardScale='column', orderRow=orderRow, orderColumn=orderColumn, showPrevalence=True, figsize=(10, 5), saveDir=saveDir, fileName=fileName, vmin=0, vmax=1)
         
-    ```
+        ```
 """
 
     # load adata