add html exports for interactive plots

docs/cli_config.rst

@@ -97,4 +97,4 @@ Running Pandora in the command line will produce a number of (intermediate) outp
     - ``*.fst``: The results of ``smartpca`` Fst computation (in case of MDS analyses)
     - In case you specified ``keep_replicates: true`` in your config, there will also be the dataset files for the windows (``*.geno``, ``*.snp``, ``*.ind``).
 
-- ``plots/``: If you set ``plot_results: true`` in your config, this directory will contain all plots Pandora generated during the execution. The names of the files should be self-explanatory.
+- ``plots/``: If you set ``plot_results: true`` in your config, this directory will contain all plots Pandora generated during the execution. The names of the files should be self-explanatory. As of version 1.0.8, we provide each plot in two formats: pdf and HTML. You can open the HTML file in any browser to see an interactive version of the plot.

pandora/pandora.py

@@ -500,6 +500,9 @@ def _plot_dataset(self, dataset: EigenDataset, plot_prefix: str) -> None:
         fig.write_image(
             self.pandora_config.plot_dir / f"{plot_prefix}_with_populations.pdf"
         )
+        fig.write_html(
+            self.pandora_config.plot_dir / f"{plot_prefix}_with_populations.html"
+        )
 
         # plot with annotated clusters
         fig = plot_clusters(
@@ -511,6 +514,9 @@ def _plot_dataset(self, dataset: EigenDataset, plot_prefix: str) -> None:
         fig.write_image(
             self.pandora_config.plot_dir / f"{plot_prefix}_with_clusters.pdf"
         )
+        fig.write_html(
+            self.pandora_config.plot_dir / f"{plot_prefix}_with_clusters.html"
+        )
 
         if len(self.dataset.embedding_populations) > 0:
             fig = plot_projections(
@@ -522,6 +528,9 @@ def _plot_dataset(self, dataset: EigenDataset, plot_prefix: str) -> None:
             fig.write_image(
                 self.pandora_config.plot_dir / f"{plot_prefix}_projections.pdf"
             )
+            fig.write_html(
+                self.pandora_config.plot_dir / f"{plot_prefix}_projections.html"
+            )
 
     def bootstrap_embeddings(self) -> None:
         """Draws bootstrap replicates of ``self.dataset`` and computes and compares the respective embedding for all
@@ -681,10 +690,13 @@ def _plot_sample_support_values(
 
         if projected_samples_only:
             fig_name = "projected_sample_support_values.pdf"
+            fig_name_html = "projected_sample_support_values.html"
         else:
             fig_name = "sample_support_values.pdf"
+            fig_name_html = "sample_support_values.html"
 
         fig.write_image(self.pandora_config.plot_dir / fig_name)
+        fig.write_html(self.pandora_config.plot_dir / fig_name_html)
         return fig
 
     def _compare_replicates_similarity(self) -> None:

tests/test_pandora.py

@@ -226,8 +226,8 @@ def test_do_pca(self, pandora_test_config):
 
         # pandora's dataset's PCA should be a PCA object now and not None
         assert isinstance(pandora.dataset.pca, PCA)
-        # plot directory should contain two plots
-        assert len(list(pandora.pandora_config.plot_dir.iterdir())) == 2
+        # plot directory should contain four plots (two pdf, two html)
+        assert len(list(pandora.pandora_config.plot_dir.iterdir())) == 4
 
     def test_do_mds(self, pandora_test_config_mds):
         pandora = Pandora(pandora_test_config_mds)
@@ -238,8 +238,8 @@ def test_do_mds(self, pandora_test_config_mds):
 
         # pandora's dataset's MDS should be a MDS object now and not None
         assert isinstance(pandora.dataset.mds, MDS)
-        # plot directory should contain two plots
-        assert len(list(pandora.pandora_config.plot_dir.iterdir())) == 2
+        # plot directory should contain four plots (two pdf, two html)
+        assert len(list(pandora.pandora_config.plot_dir.iterdir())) == 4
 
     def test_do_pca_with_pca_populations(
         self, pandora_test_config_with_embedding_populations
@@ -254,8 +254,8 @@ def test_do_pca_with_pca_populations(
         # pandora's dataset's PCA should be a PCA object now and not None
         assert isinstance(pandora.dataset.pca, PCA)
 
-        # plot directory should contain three plots
-        assert len(list(pandora.pandora_config.plot_dir.iterdir())) == 3
+        # plot directory should contain six plots (3 pdf, 3 html)
+        assert len(list(pandora.pandora_config.plot_dir.iterdir())) == 6
 
     def test_plot_dataset_fails_if_pca_is_missing(self, pandora_test_config):
         pandora = Pandora(pandora_test_config)