Update cytof/utils.py

cytof/utils.py

@@ -358,7 +358,7 @@ def check_feature_distribution(feature_summary_df, features):
 #         return None
 #     return fig
 
-def visualize_scatter(data, communities, n_community, title, figsize=(5,5), savename=None, show=False, ax=None):
+def visualize_scatter(data, communities, n_community, title, scatter_dot_size, figsize=(5,5), savename=None, show=False, ax=None):
     """
     data = data to visualize (N, 2)
     communities = group indices correspond to each sample in data (N, 1) or (N, )
@@ -372,10 +372,15 @@ def visualize_scatter(data, communities, n_community, title, figsize=(5,5), save
     else:
         fig = None
     ax.set_title(title)
-    sns.scatterplot(x=data[:,0], y=data[:,1], hue=communities, palette='tab20',
-                    hue_order=np.arange(n_community), ax=ax)
-                    #                 legend=legend,
-                    # hue_order=np.arange(n_community))
+    sns.scatterplot(x=data[:,0], 
+                    y=data[:,1], 
+                    hue=communities, 
+                    palette='tab20', 
+                    s=scatter_dot_size, 
+                    alpha=0.9, 
+                    linewidth=0,
+                    hue_order=np.arange(n_community), ax=ax
+                    )
     
     ax.legend(bbox_to_anchor=(1.01, 1), loc=2, borderaxespad=0.)
     # plt.axis('tight')
@@ -387,7 +392,7 @@ def visualize_scatter(data, communities, n_community, title, figsize=(5,5), save
         plt.show()
     if clos:
         plt.close('all')
-    return fig
+    return fig, ax
 
 def visualize_expression(data, markers, group_ids, title, figsize=(5,5), savename=None, show=False, ax=None):
     clos = not show and ax is None
@@ -403,8 +408,8 @@ def visualize_expression(data, markers, group_ids, title, figsize=(5,5), savenam
                 yticklabels=group_ids,
                 ax=ax
                )
-    ax.set_xlabel("Markers")
-    ax.set_ylabel("Phenograph clusters")
+    # ax.set_xlabel("Markers")
+    ax.set_ylabel("PhenoGraph clusters")
     ax.set_title("normalized expression - {}".format(title))
     ax.xaxis.set_tick_params(labelsize=8)
     if savename is not None:
@@ -414,7 +419,7 @@ def visualize_expression(data, markers, group_ids, title, figsize=(5,5), savenam
         plt.show()
     if clos:
         plt.close('all')
-    return fig
+    return fig, ax
 
 def _get_thresholds(df_feature: pd.DataFrame,
                     features: List[str],