1st attempt to fix rendering

scverse · Feb 5, 2024 · 8a37d15 · 8a37d15
1 parent f2241ef
commit 8a37d15
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Showing 6 changed files with 15 additions and 27 deletions.
diff --git a/pertpy/tools/_augur.py b/pertpy/tools/_augur.py
@@ -998,9 +998,6 @@ def plot_dp_scatter(
             >>> pvals = ag_rfc.predict_differential_prioritization(augur_results1=results_15, augur_results2=results_48, \
                 permuted_results1=results_15_permute, permuted_results2=results_48_permute)
             >>> ag_rfc.plot_dp_scatter(pvals)
-
-        Preview:
-        # TODO: add preview
         """
         x = results["mean_augur_score1"]
         y = results["mean_augur_score2"]
@@ -1056,9 +1053,6 @@ def plot_important_features(
             >>> loaded_data = ag_rfc.load(adata)
             >>> v_adata, v_results = ag_rfc.predict(loaded_data, subsample_size=20, select_variance_features=True, n_threads=4)
             >>> ag_rfc.plot_important_features(v_results)
-
-        Preview:
-        # TODO: add preview
         """
         if isinstance(data, AnnData):
             results = data.uns[key]
@@ -1109,9 +1103,6 @@ def plot_lollipop(
             >>> loaded_data = ag_rfc.load(adata)
             >>> v_adata, v_results = ag_rfc.predict(loaded_data, subsample_size=20, select_variance_features=True, n_threads=4)
             >>> ag_rfc.plot_lollipop(v_results)
-
-        Preview:
-        # TODO: add preview
         """
         if isinstance(data, AnnData):
             results = data.uns[key]
@@ -1160,9 +1151,6 @@ def plot_scatterplot(
             >>> h_adata, h_results = ag_rfc.predict(loaded_data, subsample_size=20, n_threads=4)
             >>> v_adata, v_results = ag_rfc.predict(loaded_data, subsample_size=20, select_variance_features=True, n_threads=4)
             >>> ag_rfc.plot_scatterplot(v_results, h_results)
-
-        Preview:
-        # TODO: add preview
         """
         cell_types = results1["summary_metrics"].columns
 

diff --git a/pertpy/tools/_coda/_base_coda.py b/pertpy/tools/_coda/_base_coda.py
@@ -1227,7 +1227,7 @@ def plot_stacked_barplot(  # pragma: no cover
             >>> sccoda.plot_stacked_barplot(mdata, feature_name="samples")
 
         Preview:
-            .. image:: ../_static/docstring_previews/sccoda_stacked_barplot.png
+            .. image:: /_static/docstring_previews/sccoda_stacked_barplot.png
         """
         if isinstance(data, MuData):
             data = data[modality_key]
@@ -1332,7 +1332,7 @@ def plot_effects_barplot(  # pragma: no cover
             >>> sccoda.plot_effects_barplot(mdata)
 
         Preview:
-            .. image:: ../_static/docstring_previews/sccoda_effects_barplot.png
+            .. image:: /_static/docstring_previews/sccoda_effects_barplot.png
         """
         if args_barplot is None:
             args_barplot = {}
@@ -1515,7 +1515,7 @@ def plot_boxplots(  # pragma: no cover
             >>> sccoda.plot_boxplots(mdata, feature_name="condition", add_dots=True)
 
         Preview:
-            .. image:: ../_static/docstring_previews/sccoda_boxplots.png
+            .. image:: /_static/docstring_previews/sccoda_boxplots.png
         """
         if args_boxplot is None:
             args_boxplot = {}
@@ -1734,7 +1734,7 @@ def plot_rel_abundance_dispersion_plot(  # pragma: no cover
             >>> sccoda.plot_rel_abundance_dispersion_plot(mdata)
 
         Preview:
-            .. image:: ../_static/docstring_previews/sccoda_rel_abundance_dispersion_plot.png
+            .. image:: /_static/docstring_previews/sccoda_rel_abundance_dispersion_plot.png
         """
         if isinstance(data, MuData):
             data = data[modality_key]

diff --git a/pertpy/tools/_dialogue.py b/pertpy/tools/_dialogue.py
@@ -1093,7 +1093,7 @@ def plot_split_violins(
             >>> dl.plot_split_violins(adata, split_key='gender', celltype_key='cell.subtypes')
 
         Preview:
-            .. image:: ../_static/docstring_previews/dialogue_violin.png
+            .. image:: /_static/docstring_previews/dialogue_violin.png
         """
         df = sc.get.obs_df(adata, [celltype_key, mcp, split_key])
         if split_which is None:
@@ -1136,7 +1136,7 @@ def plot_pairplot(
             >>> dl.plot_pairplot(adata, celltype_key="cell.subtypes", color="gender", sample_id="clinical.status")
 
         Preview:
-            .. image:: ../_static/docstring_previews/dialogue_pairplot.png
+            .. image:: /_static/docstring_previews/dialogue_pairplot.png
         """
         mean_mcps = adata.obs.groupby([sample_id, celltype_key])[mcp].mean()
         mean_mcps = mean_mcps.reset_index()

diff --git a/pertpy/tools/_enrichment.py b/pertpy/tools/_enrichment.py
@@ -326,7 +326,7 @@ def plot_dotplot(
             >>> pt_enrichment.plot_dotplot(adata, categories=["B01", "B02", "B03"], groupby="louvain")
 
         Preview:
-            .. image:: ../_static/docstring_previews/enrichment_dotplot.png
+            .. image:: /_static/docstring_previews/enrichment_dotplot.png
         """
         if categories is not None:
             if isinstance(categories, str):
@@ -403,7 +403,7 @@ def plot_gsea(
             >>> pt_enrichment.plot_gsea(adata, enrichment, interactive_plot=True)
 
         Preview:
-            .. image:: ../_static/docstring_previews/enrichment_gsea.png
+            .. image:: /_static/docstring_previews/enrichment_gsea.png
         """
         for cluster in enrichment:
             fig = blitzgsea.plot.top_table(

diff --git a/pertpy/tools/_milo.py b/pertpy/tools/_milo.py
@@ -736,7 +736,7 @@ def plot_nhood_graph(
             >>> milo.plot_nhood_graph(mdata)
 
         Preview:
-            .. image:: ../_static/docstring_previews/milo_nhood_graph.png
+            .. image:: /_static/docstring_previews/milo_nhood_graph.png
         """
         nhood_adata = mdata["milo"].T.copy()
 
@@ -809,7 +809,7 @@ def plot_nhood(
             >>> milo.plot_nhood(mdata, ix=0)
 
         Preview:
-            .. image:: ../_static/docstring_previews/milo_nhood.png
+            .. image:: /_static/docstring_previews/milo_nhood.png
         """
         mdata[feature_key].obs["Nhood"] = mdata[feature_key].obsm["nhoods"][:, ix].toarray().ravel()
         sc.pl.embedding(

diff --git a/pertpy/tools/_mixscape.py b/pertpy/tools/_mixscape.py
@@ -535,7 +535,7 @@ def plot_barplot(  # pragma: no cover
             >>> ms_pt.plot_barplot(mdata['rna'], guide_rna_column='NT')
 
         Preview:
-            .. image:: ../_static/docstring_previews/mixscape_barplot.png
+            .. image:: /_static/docstring_previews/mixscape_barplot.png
         """
         if mixscape_class_global not in adata.obs:
             raise ValueError("Please run the `mixscape` function first.")
@@ -642,7 +642,7 @@ def plot_heatmap(  # pragma: no cover
             >>> ms_pt.plot_heatmap(adata = mdata['rna'], labels='gene_target', target_gene='IFNGR2', layer='X_pert', control='NT')
 
         Preview:
-            .. image:: ../_static/docstring_previews/mixscape_heatmap.png
+            .. image:: /_static/docstring_previews/mixscape_heatmap.png
         """
         if "mixscape_class" not in adata.obs:
             raise ValueError("Please run `pt.tl.mixscape` first.")
@@ -706,7 +706,7 @@ def plot_perturbscore(  # pragma: no cover
             >>> ms_pt.plot_perturbscore(adata = mdata['rna'], labels='gene_target', target_gene='IFNGR2', color = 'orange')
 
         Preview:
-            .. image:: ../_static/docstring_previews/mixscape_perturbscore.png
+            .. image:: /_static/docstring_previews/mixscape_perturbscore.png
         """
         if "mixscape" not in adata.uns:
             raise ValueError("Please run the `mixscape` function first.")
@@ -875,7 +875,7 @@ def plot_violin(  # pragma: no cover
             >>> ms_pt.plot_violin(adata = mdata['rna'], target_gene_idents=['NT', 'IFNGR2 NP', 'IFNGR2 KO'], groupby='mixscape_class')
 
         Preview:
-            .. image:: ../_static/docstring_previews/mixscape_violin.png
+            .. image:: /_static/docstring_previews/mixscape_violin.png
         """
         if isinstance(target_gene_idents, str):
             mixscape_class_mask = adata.obs[groupby] == target_gene_idents
@@ -1057,7 +1057,7 @@ def plot_lda(  # pragma: no cover
             >>> ms_pt.plot_lda(adata=mdata['rna'], control='NT')
 
         Preview:
-            .. image:: ../_static/docstring_previews/mixscape_lda.png
+            .. image:: /_static/docstring_previews/mixscape_lda.png
         """
         if mixscape_class not in adata.obs:
             raise ValueError(f'Did not find `.obs["{mixscape_class!r}"]`. Please run the `mixscape` function first.')