exprmat 0.1.4__tar.gz → 0.1.5__tar.gz

{exprmat-0.1.4 → exprmat-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.4
+Version: 0.1.5
 Summary: routines to process expression matrices
 Home-page: https://github.com/yang-z-03/exprmat
 Author: Zheng Yang

{exprmat-0.1.4 → exprmat-0.1.5}/exprmat/plotting/expression.py

@@ -16,7 +16,7 @@ def barplot(
     colnames = ['logc' + x for x in [gene]]
     cellnames = ['c' + str(i) for i in range(len(adata.obs_names.tolist()))]
     lognorm = find_variable(adata, gene, layer = slot)
-    data = pd.DataFrame(lognorm.toarray())
+    data = pd.DataFrame(lognorm)
     
     data.columns = colnames
     if split == None: data['split'] = 'default.split'
@@ -61,7 +61,36 @@ def barplot(
     axes.set_ylabel(gene)
     axes.set_xticks(selected_groups)
     axes.set_yticks([0.0, 2.5])
-    axes.set_xticklabels(selected_groups, rotation = 45)
+
+    # axes.set_xticklabels(selected_groups, rotation = 45)
+
+    from scipy import stats
+    # here, we will run the wilcox test
+    gene_data = dropzeros.loc[dropzeros['name'] == gene,:]
+    if group != None:
+        xtl = []
+        for ct in selected_groups:
+            cell_data = gene_data.loc[gene_data['row'] == ct,:]
+            groups = [x for _, x in cell_data.groupby(cell_data['split'])]
+            values = [x['logc'].tolist() for x in groups]
+            if len(values) == 2:
+                w = stats.mannwhitneyu(values[0], values[1])
+                xtl += [ct + '\n{:.3f}'.format(w.pvalue)]
+            else: xtl += [ct]
+        
+        axes.set_xticks(selected_groups)
+        axes.set_xticklabels(xtl, rotation = 45)
+    
+    else:
+        groups = [x for _, x in gene_data.groupby(gene_data['split'])]
+        values = [x['logc'].tolist() for x in groups]
+        xtl = 'whole'
+        if len(values) == 2:
+            w = stats.mannwhitneyu(values[0], values[1])
+            xtl = 'whole\n{:.3f}'.format(w.pvalue)
+        axes.set_xticklabels([xtl], rotation = 45)
+        pass
+
     axes.spines[['left', 'top']].set_visible(False)
     axes.yaxis.set_major_formatter(ticker.StrMethodFormatter("{x:.1f}"))
     fig.tight_layout()

{exprmat-0.1.4 → exprmat-0.1.5}/exprmat/reader/experiment.py

@@ -711,6 +711,21 @@ class experiment:
         return pl.fig
     
 
+    @staticmethod
+    def rna_plot_expression_bar(
+        adata, sample_name, gene, group, split = None,
+        slot = 'X', selected_groups = None, palette = ['red', 'black'], 
+        figsize = (6,3), dpi = 100
+    ):
+        from exprmat.plotting.expression import barplot
+        pl = barplot(
+            adata, gene = gene, slot = slot, group = group,
+            split = split, selected_groups = selected_groups, palette = palette,
+            size = figsize, dpi = dpi
+        )
+        return pl
+    
+
     @staticmethod
     def rna_plot_proportion(
         adata, sample_name, major, minor, plot = 'bar', cmap = 'Turbo',
@@ -1010,6 +1025,9 @@ class experiment:
     def plot_rna_cnv_matrix(self, run_on_samples = False, **kwargs):
         return self.plot_for_rna(run_on_samples, experiment.rna_plot_cnv_matrix, **kwargs)
     
+    def plot_rna_expression_bar(self, run_on_samples = False, **kwargs):
+        return self.plot_for_rna(run_on_samples, experiment.rna_plot_expression_bar, **kwargs)
+    
 
     # accessor wrappers
 

{exprmat-0.1.4 → exprmat-0.1.5}/exprmat/utils.py

@@ -11,11 +11,11 @@ from exprmat.ansi import error
 
 
 plotting_styles = {
-    'font_name': ['Arial', 'Helvetica', 'Ubuntu', 'Verdana'],
+    'font_name': ['Helvetica Neue LT Std', 'Helvetica', 'Arial', 'Ubuntu', 'Verdana'],
     'backend': 'TkAgg'
 }
 
-def setup_styles(font_name = 'Arial', backend = 'TkAgg'):
+def setup_styles(font_name = 'Helvetica Neue LT Std', backend = 'TkAgg'):
 
     import matplotlib as mpl
     import matplotlib.pyplot as plt

{exprmat-0.1.4 → exprmat-0.1.5}/exprmat.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.4
+Version: 0.1.5
 Summary: routines to process expression matrices
 Home-page: https://github.com/yang-z-03/exprmat
 Author: Zheng Yang

{exprmat-0.1.4 → exprmat-0.1.5}/exprmat.egg-info/SOURCES.txt

@@ -9,6 +9,7 @@ exprmat.egg-info/dependency_links.txt
 exprmat.egg-info/not-zip-safe
 exprmat.egg-info/requires.txt
 exprmat.egg-info/top_level.txt
+exprmat.egg-info/.ipynb_checkpoints/requires-checkpoint.txt
 exprmat/clustering/__init__.py
 exprmat/clustering/leiden.py
 exprmat/clustering/spectral.py
@@ -23,7 +24,6 @@ exprmat/data/gff.py
 exprmat/data/private.py
 exprmat/data/ranges.py
 exprmat/data/hsa/genome.tsv.gz
-exprmat/data/mmu/gencode.tsv.gz
 exprmat/data/mmu/genome.tsv.gz
 exprmat/descriptive/__init__.py
 exprmat/descriptive/de.py

exprmat-0.1.5/exprmat.egg-info/requires.txt

@@ -0,0 +1,22 @@
+umap-learn>=0.5.0
+scvi-tools>=1.3.0
+scanpy
+anndata
+mudata
+pandas
+numpy
+matplotlib
+seaborn
+torch>=2.0
+annoy
+scikit-image
+scikit-misc
+igraph
+bbknn
+scanorama
+harmonypy
+pymde
+datashader
+fa2_modified
+pynndescent
+gseapy

{exprmat-0.1.4 → exprmat-0.1.5}/setup.py

@@ -3,7 +3,7 @@ from setuptools import setup, find_packages
 
 setup(
     name                 = 'exprmat',
-    version              = '0.1.4',
+    version              = '0.1.5',
     description          = 'routines to process expression matrices',
     url                  = 'https://github.com/yang-z-03/exprmat',
     author               = 'Zheng Yang',