exprmat 0.1.30__tar.gz → 0.1.31__tar.gz

{exprmat-0.1.30 → exprmat-0.1.31}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.30
+Version: 0.1.31
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

{exprmat-0.1.30 → exprmat-0.1.31}/exprmat/plotting/de.py

@@ -280,8 +280,8 @@ def marker_plot(
             adata,
             var_names,
             groupby,
-            show=show,
-            save=save,
+            show = False,
+            save = save,
             gene_symbols = gene_symbols,
             **kwds,
         )
@@ -293,8 +293,8 @@ def marker_plot(
             adata,
             var_names,
             groupby,
-            show=show,
-            save=save,
+            show = False,
+            save = save,
             gene_symbols = gene_symbols,
             **kwds,
         )

{exprmat-0.1.30 → exprmat-0.1.31}/exprmat/reader/experiment.py

@@ -1103,6 +1103,9 @@ class experiment:
     def plot_rna_embedding(self, run_on_samples = False, **kwargs):
         return self.plot_for_rna(run_on_samples, st.rna_plot_embedding, **kwargs)
     
+    def plot_rna_embedding_mask(self, run_on_samples = False, **kwargs):
+        return self.plot_for_rna(run_on_samples, st.rna_plot_embedding_mask, **kwargs)
+    
     def plot_rna_embedding_atlas(self, run_on_samples = False, **kwargs):
         return self.plot_for_rna(run_on_samples, st.rna_plot_embedding_atlas, **kwargs)
 

{exprmat-0.1.30 → exprmat-0.1.31}/exprmat/reader/static.py

@@ -765,6 +765,16 @@ def rna_plot_embedding(adata, sample_name, **kwargs):
     return embedding(adata, sample_name = sample_name, **kwargs)
 
 
+def rna_plot_embedding_mask(adata, sample_name, color, values, **kwargs):
+    from exprmat.reduction.plot import embedding
+    if color in adata.obs.keys():
+        adata.obs['.mask'] = [x in values for x in adata.obs[color]]
+    else: error('`color` must be within adata.obs')
+    fig = embedding(adata, sample_name = sample_name, color = '.mask', **kwargs)
+    if color in adata.obs.keys(): del adata.obs['.mask']
+    return fig
+
+
 def rna_plot_embedding_atlas(adata, sample_name, **kwargs):
     from exprmat.reduction.plot import embedding_atlas
     return embedding_atlas(adata, sample_name = sample_name, **kwargs)
@@ -782,11 +792,25 @@ def rna_plot_gene_gene_regress(adata, sample_name, **kwargs):
 def rna_plot_markers(adata, sample_name, figsize, dpi, **kwargs):
     from exprmat.plotting.de import marker_plot
     pl = marker_plot(adata, sample_name = sample_name, **kwargs)
-    pl.width = figsize[0]
-    pl.height = figsize[1]
-    pl.show()
-    pl.fig.set_dpi(dpi)
-    return pl.fig
+
+    from scanpy.plotting import DotPlot, StackedViolin, MatrixPlot
+    if isinstance(pl, DotPlot) or isinstance(pl, StackedViolin) or isinstance(pl, MatrixPlot):
+        pl.width = figsize[0]
+        pl.height = figsize[1]
+        pl.show()
+        pl.fig.set_dpi(dpi)
+        return pl.fig
+    
+    else:
+        fig = pl['heatmap_ax'].figure if 'heatmap_ax' in pl.keys() else None
+        fig = pl['track_axes'][0].figure if 'track_axes' in pl.keys() else fig
+
+        if fig:
+            fig.set_dpi(dpi)
+            fig.set_figwidth(figsize[0])
+            fig.set_figheight(figsize[1])
+            return fig
+    
 
 
 def rna_plot_expression_bar(

{exprmat-0.1.30 → exprmat-0.1.31}/pyproject.toml

@@ -18,7 +18,7 @@ description = "exprmat: Routines for expression matrices"
 readme = "readme.md"
 license = {file = "license"}
 requires-python = ">=3.9, <3.13"
-version = "0.1.30"
+version = "0.1.31"
 authors = [
     {name = "Zheng Yang", email = "xornent@outlook.com"}
 ]