tiny tweak to prevent plots from spewing in jupyter

harmslab · Dec 22, 2022 · 0fcddda · 0fcddda
1 parent dff114d
commit 0fcddda
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Showing 4 changed files with 19 additions and 8 deletions.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -49,7 +49,7 @@ Features
 Try it out on Google Colab
 ==========================
 
-+ `Go from a few initial sequences to a full alignment <https://githubtocolab.com/harmslab/topiary-examples/blob/main/notebooks/01_seed_to_alignment.ipynb>`_
++ `Go from a few initial sequences to a full alignment <https://githubtocolab.com/harmslab/topiary-examples/blob/main/notebooks/seed-to-alignment.ipynbb>`_
 + `Build a phylogenetic tree and reconstruct ancestors <https://githubtocolab.com/harmslab/topiary-examples/blob/main/notebooks/03_alignment_to_ancestors.ipynb>`_
 
 

diff --git a/topiary/draw/ancestor_data.py b/topiary/draw/ancestor_data.py
@@ -66,7 +66,8 @@ def plot_ancestor_data(df_anc,
                        alt_anc_pp=0.25,
                        width_ratio=5,
                        anc_name=None,
-                       anc_data_string=None):
+                       anc_data_string=None,
+                       close_plot=False):
     """
     Create a summary plot for an ancestor.
 
@@ -82,6 +83,8 @@ def plot_ancestor_data(df_anc,
         name of ancestor (title on graph and output file {anc_name}.pdf)
     anc_data_string : str, optional
         data to dump in subtitle
+    close_plot : bool, False
+        whether or not to close plot when complete
 
     Returns
     -------
@@ -199,4 +202,7 @@ def plot_ancestor_data(df_anc,
     if anc_name is not None:
         fig.savefig(f"{anc_name}.pdf",bbox_inches="tight")
 
+    if close_plot:
+        plt.close(fig)
+
     return fig, ax
diff --git a/topiary/raxml/ancestors.py b/topiary/raxml/ancestors.py
@@ -407,11 +407,12 @@ def _parse_raxml_anc_output(df,
                            f"# ambig gaps: {num_ambig_gaps}"]
 
         # Plot a summary of the ancestor
-        topiary.draw.plot_ancestor_data(df_list[-1],
-                                        alt_anc_pp=alt_cutoff,
-                                        width_ratio=plot_width_ratio,
-                                        anc_name=anc_name,
-                                        anc_data_string=", ".join(anc_data_string))
+        _ = topiary.draw.plot_ancestor_data(df_list[-1],
+                                            alt_anc_pp=alt_cutoff,
+                                            width_ratio=plot_width_ratio,
+                                            anc_name=anc_name,
+                                            anc_data_string=", ".join(anc_data_string),
+                                            close_plot=True)
 
 
     # Write final fasta file

diff --git a/topiary/reports/cards.py b/topiary/reports/cards.py
@@ -15,6 +15,7 @@
 
 import pandas as pd
 import numpy as np
+from matplotlib import pyplot as plt
 
 import shutil
 import os
@@ -79,10 +80,13 @@ def create_ancestor_card(anc_dict,
 
         fig, ax = plot_ancestor_data(df,
                                     width_ratio=6,
-                                    alt_anc_pp=alt_cutoff)
+                                    alt_anc_pp=alt_cutoff,
+                                    close_plot=False)
         fig.savefig(os.path.join(output_directory,f"{a}.svg"),bbox_inches = "tight")
         fig.savefig(os.path.join(output_directory,f"{a}_pp.pdf"),bbox_inches = "tight")
 
+        plt.close(fig)
+
         taxonomic = anc_dict[a]["taxonomic_dist"]
         paralog_call = anc_dict[a]["paralog_call"]