scez 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

pyproject.toml

@@ -0,0 +1,45 @@
+[tool.poetry]
+name = "scez"
+version = "0.1.2"
+authors = [
+	"Abe Arab <abarbiology@gmail.com>"
+]
+license = "MIT"
+readme = "README.md"
+description = "Single Cell Analysis, Easy Mode!"
+classifiers = [
+	"License :: OSI Approved :: MIT License"
+]
+packages = [
+	{ include = "scez" },
+	{ include = "pyproject.toml" },
+]
+
+[tool.poetry.urls]
+Source = "https://github.com/abearab/scez"
+
+[tool.poetry.dependencies]
+python = "^3.9 <4.0"
+numpy = "^1.26.0"
+pandas = "^2.1.4 <3.0.0"
+bottleneck = "^1.3.6"
+tqdm = "*"
+tomli = "*"
+matplotlib = "^3.7"
+seaborn = "^0.12.2"
+adjustText = "^0.7.3"
+scanpy = "^1.9.6"
+anndata = "^0.8.0"
+adpbulk  = "^0.1.4"
+pydeseq2 = "^0.4.0"
+pytdc = "^1.0.0"
+blitzgsea = "^1.3.0"
+
+
+[tool.poetry.group.test.dependencies]
+pytest = "*"
+tomli = "*"
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
+build-backend = "poetry_dynamic_versioning.backend"

scez/__init__.py

@@ -8,8 +8,9 @@ import scanpy as sc
 import matplotlib.pyplot as plt
 
 import tomli
+from pathlib import Path
 
-toml_dict = tomli.load(open('pyproject.toml','rb'))
+toml_dict = tomli.load(open(Path(__file__).parent.parent / 'pyproject.toml','rb'))
 __version__ = toml_dict['tool']['poetry']['version']
 
 

scez/diffexp.py

@@ -136,7 +136,8 @@ def plot_volcano(df, title=None, labels=None, n_genes=False, side='both',
         plt.show()
 
 
-def plot_top_DEG_violinplot(adata, df, title=None, labels=None, n_genes=False, side='both', font_scale=1, figsize=(10, 4), **kwargs):
+def plot_top_DEG_violinplot(adata, df, layer=None, title=None, labels=None, n_genes=False, side='both', font_scale=1, figsize=(10, 4), **kwargs):
+    
     label_font_size = 9 * font_scale
     title_font_size = 10 * font_scale
 
@@ -167,11 +168,11 @@ def plot_top_DEG_violinplot(adata, df, title=None, labels=None, n_genes=False, s
         selected_genes = df.nlargest(n_genes, '-log10(pvalue)')
 
     # Filter the single-cell dataset for the selected genes
-    subset_adata = adata[:, selected_genes.index]
+    subset_adata = adata[:, selected_genes.index].copy()
     subset_adata.var.index = subset_adata.var.index.str.split('_').str[0]
 
     # Convert the subset of adata to a DataFrame
-    subset_df = subset_adata.to_df()
+    subset_df = subset_adata.to_df(layer=layer)
 
     # Merge the DataFrame with .obs to include the 'sample' information
     merged_df = pd.merge(subset_df, adata.obs[['sample']], left_index=True, right_index=True)

{scez-0.1.0.dist-info → scez-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: scez
-Version: 0.1.0
+Version: 0.1.2
 Summary: Single Cell Analysis, Easy Mode!
 License: MIT
 Author: Abe Arab
@@ -12,22 +12,36 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: adjustText (>=0.7.3,<0.8.0)
 Requires-Dist: adpbulk (>=0.1.4,<0.2.0)
-Requires-Dist: anndata (>=0.7.4,<0.8.0)
+Requires-Dist: anndata (>=0.8.0,<0.9.0)
 Requires-Dist: blitzgsea (>=1.3.0,<2.0.0)
+Requires-Dist: bottleneck (>=1.3.6,<2.0.0)
 Requires-Dist: matplotlib (>=3.7,<4.0)
-Requires-Dist: numpy (>=1.17.0,<2.0.0)
-Requires-Dist: pandas (>=0.21,<0.22)
+Requires-Dist: numpy (>=1.26.0,<2.0.0)
+Requires-Dist: pandas (>=2.1.4,<3.0.0)
 Requires-Dist: pydeseq2 (>=0.4.0,<0.5.0)
 Requires-Dist: pytdc (>=1.0.0,<2.0.0)
+Requires-Dist: scanpy (>=1.9.6,<2.0.0)
 Requires-Dist: seaborn (>=0.12.2,<0.13.0)
+Requires-Dist: tomli
 Requires-Dist: tqdm
 Project-URL: Source, https://github.com/abearab/scez
 Description-Content-Type: text/markdown
 
 ## scez – single cell, easy mode
 [![package](https://github.com/abearab/scez/actions/workflows/main.yml/badge.svg)](https://github.com/abearab/scez/actions/workflows/main.yml)
+[![PyPI version](https://badge.fury.io/py/scez.svg)](https://badge.fury.io/py/scez)
+[![Downloads](https://static.pepy.tech/badge/scez)](https://pepy.tech/project/scez)
+[![Downloads](https://static.pepy.tech/badge/scez/month)](https://pepy.tech/project/scez)
+
+
+### Description
+There are many tools available for single-cell RNA-seq analysis, but they often require a lot of understanding of the underlying algorithms, reading of documentation, and setting up analysis environments. This takes time and effort, and can be a barrier to entry for many projects. [Single-Cell Best Practices](https://github.com/theislab/single-cell-best-practices) is a great resource for learning about the best practices for single-cell analysis. `scez` aims to provide functionalities for single-cell analysis through definitions of analysis "tasks" and implementation of these "best practices" in a user-friendly way.
+
+This is more a personal effort to streamline my own analysis workflows, but I hope it can be useful to others as well.
+
 
 ### Installation
 Make sure you have mamba installed in your base environment. If not, install it with:
@@ -36,7 +50,7 @@ conda install mamba -n base -c conda-forge
 ```
 Then, create a new conda environment with the provided `environment.yml` file and activate it. This will install all necessary dependencies for scez.
 ```bash
-conda env create -f environment.yml
+conda env create -f https://raw.githubusercontent.com/abearab/scez/main/environment.yml
 
 conda activate scez
 ```
@@ -46,6 +60,7 @@ Finally, install scez with:
 pip install scez
 ```
 
+___
 Or, if you want to install the latest version from the repository:
 ```bash
 pip install git+https://github.com/abearab/scez.git

scez-0.1.2.dist-info/RECORD

@@ -0,0 +1,12 @@
+pyproject.toml,sha256=2d1qGZM5rM0Jttr_6ZTfqe0VX6qF200vJvtIQcAZN-E,900
+scez/__init__.py,sha256=3zXd7gUTFNJK-_l89LYFI-8yqkjt99dYLmZozK6qk0c,1412
+scez/diffexp.py,sha256=q76lqldFa4_fWNmx3I1xpnurZ6drbJAIZKXf3MHVw_A,6805
+scez/preprocess.py,sha256=3iaxACkmKQjKZdaFBLRAXz1kwkNnhbdnd_gwF8rI4nw,2572
+scez/representation.py,sha256=IW0pwa_yoKf-2a3lbtxRwLTdCjB2PkS9oN4WGCLwED0,1596
+scez/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+scez/tests/test_scez.py,sha256=hoBSYB5k1WtF1hY_kyWXw1W7NolBornmTdAng6tDpjw,452
+scez/utils.py,sha256=lPmt01JILiKoBUhhxZeyhl2CfAzailTp4dIefP4FqGQ,1955
+scez-0.1.2.dist-info/LICENSE,sha256=59TS1D5RmGh66RJikXvFoq_ZW9pGirB4zUOUXLfptJM,1071
+scez-0.1.2.dist-info/METADATA,sha256=tRmPIrFKlzcb09QVpyEoU0meDAYzrZ7_0RlUd4cfTtI,2981
+scez-0.1.2.dist-info/WHEEL,sha256=RaoafKOydTQ7I_I3JTrPCg6kUmTgtm4BornzOqyEfJ8,88
+scez-0.1.2.dist-info/RECORD,,

{scez-0.1.0.dist-info → scez-0.1.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 2.0.0
 Root-Is-Purelib: true
 Tag: py3-none-any

scez-0.1.0.dist-info/RECORD

@@ -1,11 +0,0 @@
-scez/__init__.py,sha256=kmN55oxZUHJfsInsnDWvAtxSNn5KnESir65NGr_ssyo,1356
-scez/diffexp.py,sha256=V8qjqpTZVaoAb-iCa3jYmPDmDBtg5AK9OqNzRow6ic0,6770
-scez/preprocess.py,sha256=3iaxACkmKQjKZdaFBLRAXz1kwkNnhbdnd_gwF8rI4nw,2572
-scez/representation.py,sha256=IW0pwa_yoKf-2a3lbtxRwLTdCjB2PkS9oN4WGCLwED0,1596
-scez/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-scez/tests/test_scez.py,sha256=hoBSYB5k1WtF1hY_kyWXw1W7NolBornmTdAng6tDpjw,452
-scez/utils.py,sha256=lPmt01JILiKoBUhhxZeyhl2CfAzailTp4dIefP4FqGQ,1955
-scez-0.1.0.dist-info/LICENSE,sha256=59TS1D5RmGh66RJikXvFoq_ZW9pGirB4zUOUXLfptJM,1071
-scez-0.1.0.dist-info/METADATA,sha256=zpvmYCHTzCYTRyK9FfczqE6uagMQJMjv6CVukChrODU,1748
-scez-0.1.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-scez-0.1.0.dist-info/RECORD,,