exprmat 0.1.48__tar.gz → 0.1.49__tar.gz

{exprmat-0.1.48 → exprmat-0.1.49}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.48
+Version: 0.1.49
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

{exprmat-0.1.48 → exprmat-0.1.49}/exprmat/clustering/gating.py

@@ -62,3 +62,4 @@ def polygon_gate(
     df.index = df['id'].tolist()
     adata.obs[key_added] = False
     adata.obs.loc[df.index, key_added] = df['gate']
+    adata.obs[key_added] = adata.obs[key_added].astype('str').astype('category')

{exprmat-0.1.48 → exprmat-0.1.49}/exprmat/reader/experiment.py

@@ -541,6 +541,7 @@ class experiment:
                     datarows.index.name = None
                     adata.obs = adata.obs.join(datarows)
                     adata.obs_names = 'bulk-atac:' + datarows['sample']
+                    adata.obs_names.name = None
 
                     os.unlink(temp_name + '.tsv.gz')
 
@@ -781,7 +782,7 @@ class experiment:
         
         # integrate tcr metadata
         if ('rna' in merged.keys()) and os.path.exists(os.path.join(self.directory, 'tcr')):
-            self.rna_attach_tcr(merged['rna'], os.path.join(self.directory, 'tcr'))
+            st.rna_attach_tcr(merged['rna'], None, os.path.join(self.directory, 'tcr'))
 
         if 'atac' in self.modalities.keys():
             
@@ -2286,6 +2287,12 @@ class experiment:
     def plot_atac_embedding(self, run_on_samples = False, **kwargs):
         return self.plot_for_atac(run_on_samples, st.rna_plot_embedding, **kwargs)
     
+    def plot_atac_embedding_multiple(self, run_on_samples = False, **kwargs):
+        return self.plot_for_atac(run_on_samples, st.rna_plot_multiple_embedding, **kwargs)
+
+    def plot_atac_embedding_mask(self, run_on_samples = False, **kwargs):
+        return self.plot_for_atac(run_on_samples, st.rna_plot_embedding_mask, **kwargs)
+    
     def plot_atac_peaks(self, run_on_samples = False, **kwargs):
         return self.plot_for_atac(
             run_on_samples, st.atac_plot_peaks, dump = self.directory,
@@ -2295,6 +2302,11 @@ class experiment:
     def plot_atacg_embedding(self, run_on_samples = False, **kwargs):
         return self.plot_for_atac_gene_activity(run_on_samples, st.rna_plot_embedding, **kwargs)
     
+    def plot_atacg_embedding_multiple(self, run_on_samples = False, **kwargs):
+        return self.plot_for_atac_gene_activity(run_on_samples, st.rna_plot_multiple_embedding, **kwargs)
+    
+    def plot_atacg_embedding_mask(self, run_on_samples = False, **kwargs):
+        return self.plot_for_atac_gene_activity(run_on_samples, st.rna_plot_embedding_mask, **kwargs)
 
     def plot_rnaspc_qc(self, run_on_samples = False, **kwargs):
         return self.plot_for_rnaspc(run_on_samples, st.rna_plot_qc, **kwargs)

{exprmat-0.1.48 → exprmat-0.1.49}/exprmat/reader/matcher.py

@@ -771,8 +771,8 @@ def stringify_tcr(df, contig, v, d, j, nt, aa):
         else: clone = 'vj(' + df[v] + ', ' + df[j] + ')'
     
     # aa alone may show degrees of degeneration!
-    if nt is not None: clone = clone + (', ' if clone != '' else '') + 'nt(' + df[nt] + ')'
-    elif aa is not None: clone = clone + (', ' if clone != '' else '') + 'aa(' + df[aa] + ')'
+    if nt is not None: clone = clone + (', ' if not isinstance(clone, str) else '') + 'nt(' + df[nt] + ')'
+    elif aa is not None: clone = clone + (', ' if not isinstance(clone, str) else '') + 'aa(' + df[aa] + ')'
     return f'{contig}(' + clone + ')' 
 
 

{exprmat-0.1.48 → exprmat-0.1.49}/exprmat/reader/spatial.py

@@ -80,13 +80,13 @@ def read_multiscale_image_from_spatial(folder):
     
     template = {
         'images': {
-            'hires': highres / 255,
-            'lores': lowres / 255,
+            'hires': (highres / 255) if highres is not None else None,
+            'lores': (lowres / 255) if lowres is not None else None,
             'origin': None
         },
         'scalefactors': {
-            'hires': sf['tissue_hires_scalef'],
-            'lores': sf['tissue_lowres_scalef'],
+            'hires': sf['tissue_hires_scalef'] if highres is not None else None,
+            'lores': sf['tissue_lowres_scalef'] if lowres is not None else None,
             'origin': 1
         },
         'mask': None,

{exprmat-0.1.48 → exprmat-0.1.49}/exprmat/reduction/plot.py

@@ -537,7 +537,7 @@ def embedding(
 
         sb.scatterplot(
             **atlas_data, s = ptsize,
-            alpha = alpha, palette = palette, color = default_color,
+            alpha = alpha, palette = cmap, color = default_color,
             hue = labels, hue_order = None, hue_norm = hue_norm
         )
     

{exprmat-0.1.48 → exprmat-0.1.49}/pyproject.toml

@@ -20,7 +20,7 @@ description = "exprmat: Routines for expression matrices"
 readme = "readme.md"
 license = {file = "license"}
 requires-python = ">=3.9, <3.13"
-version = "0.1.48"
+version = "0.1.49"
 authors = [
     {name = "Zheng Yang", email = "xornent@outlook.com"}
 ]