Merge pull request #62 from schillerlab/fix/marker_dendrogram

refactor marker_dendrogram

sc_toolbox/api/calc/__init__.py

@@ -403,7 +403,7 @@ def correlate_means_to_gene(means: pd.DataFrame, corr_gene: str = "EOMES"):
     return cors
 
 
-def generate_extended_marker_table(
+def extended_marker_table(
     adata: AnnData,
     qval_thresh: float = 0.05,
     cell_type_label: str = "cell_type",

sc_toolbox/api/plot/__init__.py

@@ -623,23 +623,25 @@ def split_boxplot(
 
 
 def marker_dendrogram(
-    marker,
+    marker_table: pd.DataFrame,
     threshold: float = 0.7,
     column: str = "cluster",
+    log_fc_key: str = "log_FC",
     label_size: int = 10,
-    orient: str = "top",
+    orientation: str = "top",
     figsize: Tuple[int, int] = (10, 4),
     save: str = None,
 ):
     """
     Plots a dendogram of used marker genes.
 
     Args:
-        marker:
-        threshold:
-        column:
-        label_size:
-        orient:
+        marker_table: A marker table as generated by sct.calc.extended_marker_table
+        threshold: Threshold for the log fold change
+        column: Column to create pivot by; usually just the clusters
+        log_fc_key: Key for the stored log fold changes in the marker table
+        label_size: Font size of the labels
+        orientation: Orientation of the figure; Currently just 'top' or no orientation
         figsize: Size of the figure as specified in matplotlib
         save: Path to save the plot to
 
@@ -648,23 +650,22 @@ def marker_dendrogram(
     """
     import scipy.cluster.hierarchy as hc
 
-    log = "avg_logFC" if "avg_logFC" in marker.columns else "logfoldchange"
-    marker = marker[marker[log] > threshold]
+    marker_table = marker_table[marker_table[log_fc_key] > threshold]
 
-    marker = marker.pivot(index="gene", columns=column, values=log)
-    marker.fillna(value=0, inplace=True)
+    marker_table = marker_table.pivot(index="gene", columns=column, values=log_fc_key)
+    marker_table.fillna(value=0, inplace=True)
 
-    corr = 1 - marker.corr()
+    corr = 1 - marker_table.corr()
     corr = hc.distance.squareform(corr)  # convert to condensed
     z = hc.linkage(corr, method="complete")
     plt.figure(figsize=figsize)
-    rot = 90 if orient == "top" else 0
+    rot = 90 if orientation == "top" else 0
     hc.dendrogram(
         z,
-        labels=marker.columns,
+        labels=marker_table.columns,
         leaf_rotation=rot,
         color_threshold=0,
-        orientation=orient,
+        orientation=orientation,
         leaf_font_size=label_size,
         above_threshold_color="black",
     )
@@ -673,7 +674,7 @@ def marker_dendrogram(
         plt.show()
     else:
         plt.savefig("{save}")
-        print(f"Saving figure to {save}")
+        print(f"[bold blue]Saving figure to {save}")
     plt.close()