scez 0.2.1__tar.gz

scez-0.2.1/.devcontainer/Dockerfile

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+FROM continuumio/miniconda3
+
+# Install system dependencies
+USER root
+RUN apt-get update \
+  && apt-get install -y build-essential git tree curl sudo vim wget \
+  && apt-get clean \
+  && apt-get purge 
+
+# Install conda env
+COPY environment.yml /tmp/env.yaml
+
+# Install mamba in the base environment
+RUN conda config --add channels conda-forge \
+  && conda config --add channels bioconda \
+  && conda config --set channel_priority false 
+
+# Create the dev environment using mamba
+RUN conda install -y -n base -c conda-forge mamba \
+  && mamba env create -n dev -f /tmp/env.yaml \
+  && conda clean --all --yes \
+  && rm -f /tmp/env.yaml

scez-0.2.1/.devcontainer/devcontainer.json

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+{
+    "name": "scez",
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": "../"
+    },
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {
+        "version": "latest"
+        }
+    }
+}

scez-0.2.1/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for more information:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# https://containers.dev/guide/dependabot
+
+version: 2
+updates:
+ - package-ecosystem: "devcontainers"
+   directory: "/"
+   schedule:
+     interval: weekly

scez-0.2.1/.github/workflows/main.yml

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+name: Python package
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os-version }}
+    name: ${{ matrix.os-version }} (${{ matrix.python-version }})
+
+    strategy:
+      fail-fast: false
+      max-parallel: 5
+      matrix:
+        os-version: ["ubuntu-latest"]
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: "Set up Python ${{ matrix.python-version }}"
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: "Install flake8"
+      run: |
+        pip install flake8 tomli
+    - name: "Lint with flake8"
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: "Install miniconda"
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge,bioconda
+          environment-file: environment.yml
+    - name: "Install pytest"
+      shell: bash -l {0}
+      run: |
+        python -m pip install --upgrade pip
+        pip install uv
+        uv pip install --system build pytest tomli
+    - name: "Test with pytest"
+      shell: bash -l {0}
+      run: |
+        pytest -s

scez-0.2.1/.github/workflows/python-publish.yml

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+name: Publish PyPI
+
+on:
+  release:
+    types: [published]
+
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os-version }}
+    name: ${{ matrix.os-version }} (${{ matrix.python-version }})
+
+    strategy:
+      fail-fast: false
+      max-parallel: 5
+      matrix:
+        os-version: ["ubuntu-latest"]
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: "Set up Python ${{ matrix.python-version }}"
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: "Install flake8"
+      run: |
+        pip install flake8 tomli
+    - name: "Lint with flake8"
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: "Install miniconda"
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniconda-version: "latest"
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        channels: conda-forge,bioconda
+        environment-file: environment.yml
+    - name: "Install pytest"
+      shell: bash -l {0}
+      run: |
+        python -m pip install --upgrade pip
+        pip install uv
+        uv pip install --system build pytest tomli
+    - name: "Test with pytest"
+      shell: bash -l {0}
+      run: |
+        pytest -s
+    - name: Build package
+      shell: bash -l {0}
+      run: | 
+        python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}

scez-0.2.1/.gitignore

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+.idea/*
+dist/*
+build/*
+actions-runner/*
+*.lock
+**pyc
+.DS_Store
+uv.lock
+.python-version
+.venv/

scez-0.2.1/LICENSE

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+MIT License
+
+Copyright (c) 2023 Abolfazl (Abe)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

scez-0.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: scez
+Version: 0.2.1
+Summary: Single Cell Analysis, Easy Mode!
+Project-URL: Source, https://github.com/abearab/scez
+Author-email: Abe Arab <abarbiology@gmail.com>
+License: MIT
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: <4.0,>=3.9
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: tomli; extra == 'test'
+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
+
+First, create a new conda environment with the provided `environment.yml` file:
+```bash
+conda env create -f https://raw.githubusercontent.com/abearab/scez/main/environment.yml
+conda activate scez
+```
+
+Then, install scez using uv / pip:
+```bash
+uv pip install scez
+```
+
+Or, to install the latest version from the repository:
+```bash
+uv pip install git+https://github.com/abearab/scez.git
+```

scez-0.2.1/README.md

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+## 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
+
+First, create a new conda environment with the provided `environment.yml` file:
+```bash
+conda env create -f https://raw.githubusercontent.com/abearab/scez/main/environment.yml
+conda activate scez
+```
+
+Then, install scez using uv / pip:
+```bash
+uv pip install scez
+```
+
+Or, to install the latest version from the repository:
+```bash
+uv pip install git+https://github.com/abearab/scez.git
+```

scez-0.2.1/environment.yml

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+name: scez
+channels:
+  - anaconda
+  - conda-forge
+  - bioconda
+dependencies:
+  - python>=3.9
+  - scanpy
+  - pertpy
+  - python-igraph
+  - leidenalg
+  - anndata
+  - scipy
+  - scar
+  - scikit-learn
+  - matplotlib
+  - ipykernel
+  - mscorefonts
+  - pip
+  - pip:
+      - numba
+      - adpbulk
+      - pydeseq2
+      - adjustText
+      - watermark

scez-0.2.1/pyproject.toml

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+[project]
+name = "scez"
+version = "0.2.1"
+description = "Single Cell Analysis, Easy Mode!"
+authors = [
+	{ name = "Abe Arab", email = "abarbiology@gmail.com" }
+]
+license = { text = "MIT" }
+readme = "README.md"
+requires-python = ">=3.9,<4.0"
+classifiers = [
+	"License :: OSI Approved :: MIT License"
+]
+# dependencies = [
+# 	"numpy",
+# 	"pandas",
+# 	"bottleneck",
+# 	"tqdm",
+# 	"tomli",
+# 	"matplotlib",
+# 	"seaborn",
+# 	"adjustText",
+# 	"scanpy",
+# 	"anndata",
+# 	"pertpy",
+# 	"adpbulk",
+# 	"pydeseq2",
+# 	"blitzgsea",
+# ]
+
+[project.urls]
+Source = "https://github.com/abearab/scez"
+
+[project.optional-dependencies]
+test = [
+	"pytest",
+	"tomli",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

scez-0.2.1/scez/__init__.py

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+"""scez – Single Cell Analysis, Easy Mode!"""
+
+from . import diffexp as de
+from . import preprocess as pp
+from . import representation as rp
+from . import utils
+import scanpy as sc
+import matplotlib.pyplot as plt
+
+import tomli
+from pathlib import Path
+
+with open(Path(__file__).parent.parent / 'pyproject.toml', 'rb') as f:
+    toml_dict = tomli.load(f)
+__version__ = toml_dict['project']['version']
+
+
+sc.settings.verbosity = 1             # verbosity: errors (0), warnings (1), info (2), hints (3)
+sc.settings.set_figure_params(dpi=100, dpi_save=300, frameon=False, figsize=(5, 5), facecolor='white')
+sc.logging.print_header()
+
+# https://stackoverflow.com/questions/21884271/warning-about-too-many-open-figures
+plt.rcParams.update({'figure.max_open_warning': 0})
+plt.close('all')
+
+# https://stackoverflow.com/questions/3899980/how-to-change-the-font-size-on-a-matplotlib-plot
+
+SMALL_SIZE = 6
+MEDIUM_SIZE = 8
+BIGGER_SIZE = 10
+
+plt.rc('font', size=SMALL_SIZE)          # controls default text sizes
+plt.rc('axes', titlesize=SMALL_SIZE)     # font size of the axes title
+plt.rc('axes', labelsize=MEDIUM_SIZE)    # font size of the x and y labels
+plt.rc('xtick', labelsize=SMALL_SIZE)    # font size of the tick labels
+plt.rc('ytick', labelsize=SMALL_SIZE)    # font size of the tick labels
+plt.rc('legend', fontsize=SMALL_SIZE)    # legend font size
+plt.rc('figure', titlesize=BIGGER_SIZE)  # font size of the figure title

scez-0.2.1/scez/diffexp.py

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+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import seaborn as sns
+import anndata as ad
+
+from pydeseq2.dds import DeseqDataSet
+from pydeseq2.default_inference import DefaultInference
+from pydeseq2.ds import DeseqStats
+from .utils import run_adjust_text
+from adpbulk import ADPBulk
+
+
+def pseudobulk_by_clusters(adt, condition, cluster_col='leiden', method="mean"):
+    # initialize the object
+    adpb = ADPBulk(adt, [cluster_col, condition], method=method)
+
+    # perform the pseudobulking
+    pseudobulk_matrix = adpb.fit_transform()
+
+    # retrieve the sample metadata (useful for easy incorporation with edgeR)
+    sample_meta = adpb.get_meta()
+
+    out = ad.AnnData(
+        X=pseudobulk_matrix,
+        obs=sample_meta.set_index('SampleName')
+    )
+
+    return out
+
+
+def run_deseq(adata, design, tested_level, ref_level, n_cpus=8):
+
+    inference = DefaultInference(n_cpus=n_cpus)
+    
+    dds = DeseqDataSet(
+        counts=adata.to_df().astype(int),
+        metadata=adata.obs,
+        design_factors=design,  # compare samples based on the "condition"
+        refit_cooks=True,
+        inference=inference,
+    )
+
+    dds.deseq2()
+
+    stat_res = DeseqStats(
+        dds, 
+        contrast=[design, tested_level, ref_level], 
+        inference=inference
+    )
+    stat_res.summary()
+
+    df = stat_res.results_df
+
+    return df
+
+
+def plot_volcano(df, title=None, labels=None, n_genes=False, side='both', 
+                 font_scale=1, dot_size = 5,
+                 color = '#1f77b4', color_highlight = '#FFA500',
+                 ax = None, **kwargs):
+    dot_size_highlight = dot_size * 1.1
+    annotate_font_size = 5 * font_scale
+    scatter_font_size = 8 * font_scale
+    label_font_size = 9 * font_scale
+    title_font_size = 10 * font_scale
+
+    if 'name' not in df.columns: df['name'] = df.index.to_list()
+    df['-log10(pvalue)'] = - np.log10(df.pvalue)
+
+    if not ax: fig, ax = plt.subplots(figsize=(3, 3))
+
+    # Scatter plot
+    ax.scatter(
+        df['log2FoldChange'],
+        df['-log10(pvalue)'],
+        alpha=0.9, s=dot_size, c=color,
+        **kwargs
+    )
+
+    # Set background color to transparent
+    ax.set_facecolor('none')
+
+    # Set smaller font size
+    ax.tick_params(axis='both', which='both', labelsize=scatter_font_size)
+
+    # Set labels
+    ax.set_xlabel('log2FoldChange', fontsize=label_font_size)
+    ax.set_ylabel('-log10(pvalue)', fontsize=label_font_size)
+
+    # Set plot title
+    if not title:
+        ax.set_title('Volcano Plot', fontsize=title_font_size)
+    else:
+        ax.set_title(title, fontsize=title_font_size)
+
+    ax.grid(False)
+
+    # check if `labels` is provided or set that based on `n_genes` and `side`
+    if labels and n_genes:
+        # error message if both labels and n_genes are provided and say one of them is allowed
+        raise ValueError('Provide either labels or n_genes, not both!')
+
+    elif n_genes and side == 'positive':
+        # Highlight top genes
+        top_genes = df.query('log2FoldChange > 0').nlargest(n_genes, '-log10(pvalue)')
+        labels = [row['name'] for _, row in top_genes.iterrows()]
+
+    elif n_genes and side == 'negative':
+        # Highlight top genes
+        top_genes = df.query('log2FoldChange < 0').nlargest(n_genes, '-log10(pvalue)')
+        labels = [row['name'] for _, row in top_genes.iterrows()]
+
+    elif n_genes and side == 'both':
+        # Highlight top genes
+        top_genes = df.nlargest(n_genes, '-log10(pvalue)')
+        labels = [row['name'] for _, row in top_genes.iterrows()]
+
+    # Highlight the points from given labels
+    if labels:
+        for label in labels:
+            ax.scatter(
+                df.loc[label, 'log2FoldChange'],
+                df.loc[label, '-log10(pvalue)'],
+                s=dot_size_highlight, c=color_highlight
+            )
+        run_adjust_text(
+            df.loc[labels, 'log2FoldChange'], 
+            df.loc[labels, '-log10(pvalue)'], 
+            labels, 
+            font_size=annotate_font_size, ax=ax, use_arrow=False
+        )
+
+    if not ax: 
+        plt.tight_layout()
+        plt.show()
+
+
+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
+
+    if 'name' not in df.columns: df['name'] = df.index.to_list()
+
+    if labels and n_genes:
+        # error message if both labels and n_genes are provided and say one of them is allowed
+        raise ValueError('Provide either labels or n_genes, not both!')
+
+    if not labels and not n_genes:
+        # error message if neither labels nor n_genes are provided
+        raise ValueError('Provide either labels or n_genes!')
+
+    if labels:
+        # Highlight the points from given list
+        selected_genes = df.loc[labels]
+
+    elif n_genes and side == 'positive':
+        # Highlight top genes
+        selected_genes = df.query('log2FoldChange > 0').nlargest(n_genes, '-log10(pvalue)')
+
+    elif n_genes and side == 'negative':
+        # Highlight top genes
+        selected_genes = df.query('log2FoldChange < 0').nlargest(n_genes, '-log10(pvalue)')
+
+    elif n_genes and side == 'both':
+        # Highlight top genes
+        selected_genes = df.nlargest(n_genes, '-log10(pvalue)')
+
+    # Filter the single-cell dataset for the selected genes
+    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(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)
+
+    # Melt the DataFrame to prepare for violin plot
+    melted_df = pd.melt(merged_df, id_vars='sample', var_name='Gene', value_name='Counts')
+
+    # Create a violin plot
+    plt.figure(figsize=figsize)
+    sns.violinplot(x='Gene', y='Counts', hue='sample', data=melted_df, split=True, inner='quartile', palette='Set2', **kwargs)
+    sns.stripplot(x='Gene', y='Counts', hue='sample', data=melted_df, dodge=True, jitter=True, color='black', size=1, alpha=0.3, **kwargs)
+
+    plt.xticks(rotation=45, ha='right', fontsize=label_font_size)
+    plt.legend(bbox_to_anchor=(1.05, 1), loc='upper left', fontsize=label_font_size)
+
+    if not title:
+        plt.title('Top Differentially Expressed Genes', fontsize=title_font_size)
+    else:
+        plt.title(title, fontsize=title_font_size)
+    plt.show()
+
+
+def write_top_DEGs(df, sample_id, result_dir='.', n_hits=200):
+    df['-log10(pvalue)'] = - np.log10(df.pvalue)
+    df.nlargest(n_hits, '-log10(pvalue)').to_csv(f'{result_dir}/{sample_id}_top_{n_hits}.csv')  # Adjust the number as needed

scez-0.2.1/scez/preprocess.py

@@ -0,0 +1,74 @@
+import pandas as pd
+import scanpy as sc
+import scar
+
+
+def normalization(adata, target_sum=1e4, max_value=10, final_layer='scaled', keep_initial_layer=True):
+    if keep_initial_layer == True:
+        adata.layers['raw_counts'] = adata.X.copy()
+    elif type(keep_initial_layer) == str:
+        adata.layers[keep_initial_layer] = adata.X.copy()
+    
+    # normalize counts to target_sum (default 1e4)
+    counts = sc.pp.normalize_total(adata, target_sum=target_sum, inplace=False)
+    # log1p transform
+    adata.layers["log1p_norm"] = sc.pp.log1p(counts["X"], copy=True)
+    # scale counts
+    adata.layers['scaled'] = sc.pp.scale(adata, max_value=max_value, copy=True).X
+    # set the final layer
+    adata.X = adata.layers[final_layer]
+
+
+def remove_ambient_rna(adata_filtered_feature_bc, adata_raw_feature_bc):
+    scar.setup_anndata(
+        adata = adata_filtered_feature_bc,
+        raw_adata = adata_raw_feature_bc,
+        prob = 0.995,
+        kneeplot = True
+    )
+
+    adata_scar = scar.model(
+        raw_count=adata_filtered_feature_bc.to_df(), # In the case of Anndata object, scar will automatically use the estimated ambient_profile present in adata.uns.
+        # ambient_profile=adata_filtered_feature_bc.uns['ambient_profile_Gene Expression'],
+        feature_type='mRNA',
+        sparsity=1,
+        # device=device # Both cpu and cuda are supported.
+    )
+
+    adata_scar.train(
+        epochs=200,
+        batch_size=64,
+        verbose=True
+    )
+
+    # After training, we can infer the native true signal
+    adata_scar.inference(batch_size=256)  # by defaut, batch_size = None, set a batch_size if getting a memory issue
+
+    denoised_count = pd.DataFrame(
+        adata_scar.native_counts, 
+        index=adata_filtered_feature_bc.obs_names, 
+        columns=adata_filtered_feature_bc.var_names
+    )
+
+    adata = adata_filtered_feature_bc.copy()
+    adata.layers['raw_counts'] = adata.X
+    adata.layers['scar_denoised_counts'] = denoised_count.to_numpy()
+
+    return adata
+
+
+def clustering(
+        adata
+        ):
+    pass
+    # , n_pcs=50, n_neighbors=30, use_highly_variable='Yes',
+    #     use_rep=None, resolution=None
+    
+    # if use_highly_variable == 'Yes':
+    #     sc.pp.highly_variable_genes(adata, min_mean=0.0125, max_mean=3, min_disp=0.5)
+    #     sc.tl.pca(adata, svd_solver='arpack', use_highly_variable=True)
+    # else:
+    #     sc.pp.pca(adata, n_comps=n_pcs)
+    # sc.pp.neighbors(adata, use_rep=use_rep, n_neighbors=n_neighbors)#, n_pcs=n_pcs)
+    # sc.tl.umap(adata)
+    # sc.tl.leiden(adata, resolution=resolution)

scez-0.2.1/scez/representation.py

@@ -0,0 +1,44 @@
+from itertools import product
+import matplotlib.pyplot as plt
+import scanpy as sc
+import numpy as np
+
+
+def optimising_umap_layout(adata, cluster_key='leiden',MIN_DISTS = [0.1, 1, 2], SPREADS = [0.5, 1, 5]):
+    # https://scanpy-tutorials.readthedocs.io/en/latest/plotting/advanced.html
+    # Copy adata not to modify UMAP in the original adata object
+    adata_temp = adata.copy()
+    
+    # Create grid of plots, with a little extra room for the legends
+    fig, axes = plt.subplots(
+        len(MIN_DISTS), len(SPREADS), figsize=(len(SPREADS) * 3 + 2, len(MIN_DISTS) * 3)
+    )
+
+    # Loop through different umap parameters, recomputting and replotting UMAP for each of them
+    for (i, min_dist), (j, spread) in product(enumerate(MIN_DISTS), enumerate(SPREADS)):
+        ax = axes[i][j]
+        param_str = " ".join(["min_dist =", str(min_dist), "and spread =", str(spread)])
+        # Recompute UMAP with new parameters
+        sc.tl.umap(adata_temp, min_dist=min_dist, spread=spread)
+        # Create plot, placing it in grid
+        sc.pl.umap(
+            adata_temp,
+            color=[cluster_key],
+            title=param_str,
+            s=40,
+            ax=ax,
+            show=False,
+        )
+    plt.tight_layout()
+    plt.show()
+    plt.close()
+    del adata_temp
+
+
+def random_ordering(adata):
+    # Randomly order cells by making a random index and subsetting AnnData based on it
+    # Set a random seed to ensure that the cell ordering will be reproducible
+    np.random.seed(0)
+    random_indices = np.random.permutation(list(range(adata.shape[0])))
+
+    return random_indices

scez-0.2.1/scez/tests/test_scez.py

@@ -0,0 +1,19 @@
+import unittest
+import matplotlib.pyplot as plt
+import scanpy as sc
+import scez
+import tomli
+
+with open('pyproject.toml', 'rb') as f:
+    toml_dict = tomli.load(f)
+version = toml_dict['project']['version']
+
+class TestScezConfig(unittest.TestCase):
+    def test_version(self):
+        self.assertEqual(scez.__version__, version)
+
+    def test_scanpy_settings(self):
+        self.assertEqual(sc.settings.verbosity, 1)
+
+if __name__ == '__main__':
+    unittest.main()

scez-0.2.1/scez/utils.py

@@ -0,0 +1,64 @@
+import pandas as pd
+from matplotlib import pyplot as plt
+from adjustText import adjust_text
+
+
+def rank_genes_to_df(adata, n=50):
+    result = adata.uns['rank_genes_groups']
+
+    groups = result['names'].dtype.names
+
+    df = pd.DataFrame(
+        {group + '_' + key: result[key][group]
+         for group in groups for key in ['names', 'scores']}).head(n)
+
+    return df
+
+
+def add_marker_feature(adata, marker, marker_name, clusters_name, thr = 0, figsize=(10, 4)):
+
+    adata.obs[marker_name] = ''
+    adata.obs.loc[adata.to_df().loc[:,marker] <= thr, marker_name] = f'{marker}-'
+    adata.obs.loc[adata.to_df().loc[:,marker] > thr, marker_name] = f'{marker}+'
+
+    df = pd.concat([
+        adata.obs.groupby([marker_name,clusters_name]).size()[f'{marker}+'],
+        adata.obs.groupby([marker_name,clusters_name]).size()[f'{marker}-']
+    ],axis=1).rename(columns={0:f'{marker}+',1:f'{marker}-'})
+
+    # Make some labels.
+    labels = df[f'{marker}+'] / df.sum(axis=1) * 100
+    labels = labels.round(decimals=1)
+    labels.sort_values(ascending=False,inplace=True)
+    df = df.loc[labels.index,]
+
+    ax = df.plot.bar(stacked=True,rot=0,figsize=figsize)
+
+    rects = ax.patches
+
+    for rect, label in zip(rects, labels):
+        height = rect.get_height()
+        ax.text(
+            rect.get_x() + rect.get_width() / 2, height + 5, str(label) + "%",
+            ha="center", va="bottom", fontsize=8
+        )
+
+    ax.set_yscale('log')
+    ax.set_ylabel('# of cells')
+    return ax
+
+
+def run_adjust_text(x, y, labels, ax=None, use_arrow=True, font_weight='bold', font_size=8):
+    texts = [
+        plt.text(
+            x[i], y[i], 
+            labels[i],
+            fontdict={'weight': font_weight, 'size': font_size},
+            ha='center', va='center'
+        ) for i in range(len(x))
+    ]
+    
+    if use_arrow:
+        adjust_text(texts, arrowprops=dict(arrowstyle='->', color='red'), ax = ax)
+    else:
+        adjust_text(texts, ax = ax)

scez-0.2.1/setup-miniconda-patched-environment.yml

@@ -0,0 +1,26 @@
+name: scez
+channels:
+  - anaconda
+  - conda-forge
+  - bioconda
+dependencies:
+  - python>=3.9
+  - scanpy
+  - pertpy
+  - python-igraph
+  - leidenalg
+  - anndata
+  - scipy
+  - scar
+  - scikit-learn
+  - matplotlib
+  - ipykernel
+  - mscorefonts
+  - pip
+  - pip:
+      - numba
+      - adpbulk
+      - pydeseq2
+      - adjustText
+      - watermark
+  - python=3.12