adding plot tests

scimap/plotting/cluster_plots.py

@@ -67,7 +67,8 @@ def cluster_plots (adata,
                    subsample=100000, 
                    palette ='viridis', 
                    use_raw=False,
-                   size=None, output_dir=None):
+                   size=None, 
+                   output_dir=None):
     """
 Parameters:
         adata (anndata.AnnData):  

scimap/plotting/densityPlot2D.py

@@ -22,6 +22,8 @@
 import copy
 from matplotlib import cm
 from matplotlib.colors import LogNorm
+import os
+
 mpl.rcParams['pdf.fonttype'] = 42
 
 
@@ -38,8 +40,8 @@ def densityPlot2D (adata,
                    dpi=100, 
                    xticks=None,
                    yticks=None,
-                   outputDir=None, 
-                   outputFileName='densityPlot2D.pdf'):
+                   saveDir=None, 
+                   fileName='densityPlot2D.pdf'):
 
     """
 Parameters:
@@ -92,10 +94,10 @@ def densityPlot2D (adata,
     yticks (list of float, optional):  
         Custom y-axis tick values.
 
-    outputDir (str, optional):  
+    saveDir (str, optional):  
         The directory to save the output plot.
 
-    outputFileName (str, optional):  
+    fileName (str, optional):  
         The name of the output file. Use desired file format as suffix (e.g. `.png` or `.pdf`).
 
 Returns:
@@ -226,9 +228,15 @@ def calculate_grid_dimensions(num_items, num_columns=None):
     plt.tight_layout()
 
     # Save the figure to a file
-    # save figure
-    if outputDir is not None:
-        plt.savefig(pathlib.Path(outputDir) / outputFileName)
+    if saveDir:
+        if not os.path.exists(saveDir):
+            os.makedirs(saveDir)
+        full_path = os.path.join(saveDir, fileName)
+        plt.savefig(full_path, dpi=300)
+        plt.close(fig)
+        print(f"Saved heatmap to {full_path}")
+    else:
+        plt.show()
 
 
 

scimap/plotting/distPlot.py

@@ -17,6 +17,8 @@
 import itertools
 import pathlib
 import matplotlib as mpl
+import os
+
 mpl.rcParams['pdf.fonttype'] = 42
 
 def distPlot(adata, 
@@ -32,8 +34,8 @@ def distPlot(adata,
              figsize=(5, 5), 
              fontsize=None, 
              dpi=200, 
-             outputDir=None, 
-             outputFileName='scimapDistPlot.png'):
+             saveDir=None, 
+             fileName='scimapDistPlot.png'):
 
     """
 Parameters:
@@ -79,10 +81,10 @@ def distPlot(adata,
     dpi (int, optional):  
         The DPI of the figure. Use this to control the point size. Lower the dpi, larger the point size.
     
-    outputDir (str, optional):  
+    saveDir (str, optional):  
         The directory to save the output plot.
 
-    outputFileName (str, optional):  
+    fileName (str, optional):  
         The name of the output file. Use desired file format as suffix (e.g. `.png` or `.pdf`).
 
 Returns:
@@ -233,8 +235,16 @@ def calculate_grid_dimensions(num_items, num_columns=None):
         plt.tight_layout()
 
         # Save the figure to a file
-        # save figure
-        if outputDir is not None:
-            plt.savefig(pathlib.Path(outputDir) / outputFileName)
-
+        if saveDir:
+            if not os.path.exists(saveDir):
+                os.makedirs(saveDir)
+            full_path = os.path.join(saveDir, fileName)
+            plt.savefig(full_path, dpi=300)
+            plt.close()
+            print(f"Saved heatmap to {full_path}")
+        else:
+            plt.show()
+
+
+
 

scimap/plotting/foldchange.py

@@ -20,6 +20,8 @@
 import matplotlib.pyplot as plt 
 import numpy as np
 from pandas.plotting import parallel_coordinates
+import os
+
 sns.set_style("white")
 
 import matplotlib as mpl
@@ -42,6 +44,8 @@ def foldchange (adata,
                 matplotlib_legend_loc='upper left',
                 xticks_rotation=90,
                 return_data = False,
+                fileName='foldchange.pdf',
+                saveDir=None,
                 **kwargs):
     """
 Parameters:
@@ -165,9 +169,9 @@ def foldchange (adata,
     if method == 'heatmap':
         # heatmap of the foldchange
         #g= sns.clustermap(fold, cmap=cmap, mask=mask, center=center, col_cluster=False, row_cluster=False)
-        g= sns.clustermap(fold, cmap=cmap, mask=mask, center=center, **kwargs)
+        fig= sns.clustermap(fold, cmap=cmap, mask=mask, center=center, **kwargs)
         plt.suptitle('reference: '+ str(ref))
-        plt.setp(g.ax_heatmap.get_xticklabels(), rotation=xticks_rotation)
+        plt.setp(fig.ax_heatmap.get_xticklabels(), rotation=xticks_rotation)
         plt.tight_layout()
 
 
@@ -186,6 +190,17 @@ def foldchange (adata,
         plt.xticks(rotation = xticks_rotation)
         plt.suptitle('reference: '+ str(ref))
         fig.tight_layout()
+
+    # save
+    if saveDir:
+        if not os.path.exists(saveDir):
+            os.makedirs(saveDir)
+        full_path = os.path.join(saveDir, fileName)
+        plt.savefig(full_path, dpi=300)
+        plt.close()
+        print(f"Saved plot to {full_path}")
+    else:
+        plt.show()
 
     # return data
     if return_data is True:

scimap/plotting/groupCorrelation.py

@@ -124,7 +124,7 @@ def groupCorrelation(adata,
         adata = ad.read_h5ad(adata)
 
     # Calculate group counts
-    group_counts = adata.obs.groupby([condition, groupBy]).size().unstack(fill_value=0)
+    group_counts = adata.obs.groupby([condition, groupBy], observed=False).size().unstack(fill_value=0)
 
     # Subset groups if needed
     if subsetGroups:
@@ -190,13 +190,12 @@ def groupCorrelation(adata,
     plt.tight_layout()
 
     # Save or show the figure
-    if saveDir and fileName:
+    if saveDir:
         if not os.path.exists(saveDir):
             os.makedirs(saveDir)
         full_path = os.path.join(saveDir, fileName)
         plt.savefig(full_path, dpi=300)
-        if not os.path.exists(saveDir):
-            os.makedirs(saveDir)
+        plt.close()
         print(f"Saved heatmap to {full_path}")
     else:
         plt.show()

scimap/plotting/heatmap.py

@@ -46,7 +46,7 @@ def heatmap (adata,
              cmap='vlag',
              figsize=None,
              saveDir=None, 
-             fileName=None,
+             fileName='heatmap.pdf',
              verbose=True,
              **kwargs
              ):
@@ -312,7 +312,7 @@ def plot_category_heatmap_vectorized(data,
         plt.tight_layout(rect=[0, 0, 0.9, 0.9]) # Adjust the layout
 
         # Saving the figure if saveDir and fileName are provided
-        if saveDir and fileName:
+        if saveDir:
             if not os.path.exists(saveDir):
                 os.makedirs(saveDir)
             full_path = os.path.join(saveDir, fileName)

scimap/plotting/markerCorrelation.py

@@ -189,12 +189,13 @@ def markerCorrelation (adata,
     plt.tight_layout()
 
     # Saving the figure if saveDir and fileName are provided
-    if saveDir and fileName:
+    if saveDir:
         if not os.path.exists(saveDir):
             os.makedirs(saveDir)
         full_path = os.path.join(saveDir, fileName)
         plt.savefig(full_path, dpi=300)
-        print(f"Saved heatmap to {full_path}")
+        plt.close()
+        print(f"Saved plot to {full_path}")
     else:
         plt.show()
 

scimap/plotting/umap.py

@@ -28,6 +28,7 @@
 import matplotlib.colors as colors
 import seaborn as sns
 import matplotlib.patches as mpatches
+import os
 
 plt.rcParams['figure.dpi'] = 100
 plt.rcParams['savefig.dpi']=300
@@ -50,7 +51,9 @@ def umap (adata,
           ncols=None, 
           tight_layout=False, 
           return_data=False, 
-          save_figure=None, **kwargs):
+          saveDir=None, 
+          fileName = 'umap.pdf',
+          **kwargs):
     """
 Parameters:
         adata (anndata.AnnData):  
@@ -96,7 +99,7 @@ def umap (adata,
         return_data (bool, optional):  
             If True, returns the DataFrame containing data used for plotting instead of displaying the plot.
 
-        save_figure (str, optional):  
+        saveDir (str, optional):  
             Path and filename to save the figure. File extension determines the format (e.g., `.pdf`, `.png`).
 
         **kwargs:  
@@ -311,8 +314,15 @@ def umap (adata,
             k = k+1 # iterator
 
     # if save figure is requested
-    if save_figure is not None:
-        plt.savefig(save_figure)  
+    if saveDir:
+        if not os.path.exists(saveDir):
+            os.makedirs(saveDir)
+        full_path = os.path.join(saveDir, fileName)
+        plt.savefig(full_path, dpi=300)
+        plt.close(fig)
+        print(f"Saved heatmap to {full_path}")
+    else:
+        plt.show()
 
     # return data if needed
     if return_data is True:

scimap/tests/test_pl.py

@@ -30,17 +30,89 @@ def test_heatmap (adata):
     full_path = os.path.join(saveDir, fileName)
     assert os.path.exists(full_path), f"File was not created: {full_path}"
 
+# markerCorrelation
+def test_markerCorrelation (adata):
+    from scimap.plotting.markerCorrelation import markerCorrelation
+    saveDir = os.getcwd() + '/testFigures'
+    fileName = 'markerCorrelation.png'
+    markerCorrelation(adata, saveDir=saveDir, fileName=fileName)
+    # check the file exist
+    full_path = os.path.join(saveDir, fileName)
+    assert os.path.exists(full_path), f"File was not created: {full_path}"
 
 
+# groupCorrelation
+def test_groupCorrelation (adata):
+    from scimap.plotting.groupCorrelation import groupCorrelation
+    saveDir = os.getcwd() + '/testFigures'
+    fileName = 'groupCorrelation.png'
+    groupCorrelation(adata, groupBy='ROI', condition='phenotype', saveDir=saveDir, fileName=fileName)
+    # check the file exist
+    full_path = os.path.join(saveDir, fileName)
+    assert os.path.exists(full_path), f"File was not created: {full_path}"
 
 
-# markerCorrelation
-# groupCorrelation
 # distPlot
+def test_distPlot (adata):
+    from scimap.plotting.distPlot import distPlot
+    saveDir = os.getcwd() + '/testFigures'
+    fileName = 'distPlot.png'
+    distPlot(adata, markers=['ECAD','FOXP3'], plotGrid=True, ncols=2, saveDir=saveDir, fileName=fileName)
+    # check the file exist
+    full_path = os.path.join(saveDir, fileName)
+    assert os.path.exists(full_path), f"File was not created: {full_path}"
+
+
 # densityPlot2D
+def test_densityPlot2D (adata):
+    from scimap.plotting.densityPlot2D import densityPlot2D
+    saveDir = os.getcwd() + '/testFigures'
+    fileName = 'densityPlot2D.png'
+    densityPlot2D(adata, markerA='ECAD', markerB='FOXP3',saveDir=saveDir, fileName=fileName)
+    # check the file exist
+    full_path = os.path.join(saveDir, fileName)
+    assert os.path.exists(full_path), f"File was not created: {full_path}"
+
+
 # cluster_plots
+def test_cluster_plots (adata):
+    from scimap.plotting.cluster_plots import cluster_plots
+    output_dir = os.getcwd() + '/testFigures'
+    fileName = '_matrixplot.pdf'
+    cluster_plots(adata, group_by='phenotype', output_dir=output_dir)
+    # check the file exist
+    full_path = os.path.join(output_dir, fileName)
+    assert os.path.exists(full_path), f"File was not created: {full_path}"
+
+
 # umap
+def test_umap (adata):
+    from scimap.plotting.umap import umap
+    saveDir = os.getcwd() + '/testFigures'
+    fileName = 'umap.png'
+    umap(adata, color='phenotype', saveDir=saveDir, fileName=fileName)
+    # check the file exist
+    full_path = os.path.join(saveDir, fileName)
+    assert os.path.exists(full_path), f"File was not created: {full_path}"
+
+
 # foldchange
+def test_foldchange (adata):
+    from scimap.tools.foldchange import foldchange
+    adata = foldchange(adata, from_group = 'ROI1', imageid='ROI')
+    # plotting
+    from scimap.plotting.foldchange import foldchange
+    saveDir = os.getcwd() + '/testFigures'
+    fileName = 'foldchange.png'
+    foldchange(adata, label='foldchange', method='heatmap', saveDir=saveDir, fileName=fileName)
+    # check the file exist
+    full_path = os.path.join(saveDir, fileName)
+    assert os.path.exists(full_path), f"File was not created: {full_path}"
+
+
+
+
+
 # spatial_scatterPlot
 # spatial_distance
 # spatial_interaction