exprmat 0.1.32__tar.gz → 0.1.33__tar.gz

{exprmat-0.1.32 → exprmat-0.1.33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.32
+Version: 0.1.33
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -56,10 +56,17 @@ Requires-Dist: graphtools
 Requires-Dist: bincsync>=0.3.0
 Requires-Dist: pybigwig
 Requires-Dist: loompy
+Requires-Dist: squidpy
+Requires-Dist: zarr
+Requires-Dist: spatialdata-io
+Requires-Dist: scikit-image
+Requires-Dist: spatial-image
+Requires-Dist: multiscale-spatial-image
+Requires-Dist: tangram-sc
 Requires-Dist: sphinx ; extra == 'dev'
-Requires-Dist: sphinx-rtd-theme ; extra == 'dev'
 Requires-Dist: twine ; extra == 'dev'
 Requires-Dist: ipykernel ; extra == 'dev'
+Requires-Dist: ipytree ; extra == 'dev'
 Provides-Extra: dev
 License-File: license
 Summary: exprmat: Routines for expression matrices

{exprmat-0.1.32 → exprmat-0.1.33}/exprmat/plotting/expression.py

@@ -171,14 +171,14 @@ def volcano(
     import numpy as np
     import matplotlib.pyplot as plt
     from adjustText import adjust_text
-    from exprmat.reader.experiment import experiment
+    import exprmat.reader.static as st
 
     pvals = []
     fc = []
     names = []
 
     if isinstance(de_slot, str):
-        plots = experiment.rna_get_markers(
+        plots = st.rna_get_markers(
             adata, de_slot = de_slot,
             min_pct = min_pct, max_pct_reference = max_pct_reference, 
             min_lfc = min_lfc, max_lfc = max_lfc, 

{exprmat-0.1.32 → exprmat-0.1.33}/exprmat/plotting/gse.py

@@ -510,7 +510,7 @@ class dotplot(object):
         figsize: Tuple[float, float] = (6, 5.5),
         cmap: str = 'turbo',
         marker: str = "o",
-        formatter = None,
+        formatter = lambda x: x,
         ** kwargs,
     ):
         
@@ -827,7 +827,7 @@ def gsea_dotplot(
     yticklabels_rot: Optional[float] = None,
     marker: str = "o",
     show_ring: bool = False,
-    formatter = None,
+    formatter = lambda x: x,
     **kwargs,
 ):
     
@@ -885,7 +885,7 @@ def opa_dotplot(
     yticklabels_rot: Optional[float] = None,
     marker: str = "o",
     show_ring: bool = False,
-    formatter = None,
+    formatter = lambda x: x,
     **kwargs,
 ):
     

{exprmat-0.1.32 → exprmat-0.1.33}/exprmat/reader/static.py

@@ -1231,7 +1231,7 @@ def rna_plot_gsea_running_es(
 def rna_plot_gsea_dotplot(
     adata, sample_name, gsea_key, max_fdr = 1, max_p = 0.05, top_term: int = 100,
     colour = 'p', title = "", cmap = 'turbo', figsize = (3, 2), cutoff = 1, ptsize = 5,
-    terms = None, formatter = None
+    terms = None, formatter = lambda x: x
 ):
     from exprmat.plotting.gse import gsea_dotplot
     return gsea_dotplot(
@@ -1245,7 +1245,7 @@ def rna_plot_gsea_dotplot(
 def rna_plot_opa_dotplot(
     adata, sample_name, opa_key, max_fdr = 1, max_p = 0.05, top_term: int = 100, terms = None,
     colour = 'fdr', title = None, cmap = 'turbo', figsize = (3, 2), cutoff = 1, ptsize = 5,
-    formatter = None
+    formatter = lambda x: x
 ):
     from exprmat.plotting.gse import opa_dotplot
     return opa_dotplot(

{exprmat-0.1.32 → exprmat-0.1.33}/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 = "0.1.32"
+version = "0.1.33"
 authors = [
     {name = "Zheng Yang", email = "xornent@outlook.com"}
 ]
@@ -81,15 +81,22 @@ dependencies = [
     'graphtools',
     'bincsync >= 0.3.0',
     'pyBigWig',
-    'loompy'
+    'loompy',
+    'squidpy',
+    'zarr',
+    'spatialdata-io',
+    'scikit-image',
+    'spatial-image',
+    'multiscale-spatial-image',
+    'tangram-sc'
 ]
 
 [project.optional-dependencies]
 dev = [
     'sphinx',
-    'sphinx-rtd-theme',
     'twine',
-    'ipykernel'
+    'ipykernel',
+    'ipytree'
 ]
 
 [project.urls]