rectanglepy 0.5.0__tar.gz → 0.5.2__tar.gz

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.0
+current_version = 0.5.2
 tag = True
 commit = True
 

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/.github/workflows/build.yaml

@@ -23,6 +23,10 @@ jobs:
                 include:
                     - os: ubuntu-latest
                       python: "3.10"
+                    - os: ubuntu-latest
+                      python: "3.11"
+                    - os: ubuntu-latest
+                      python: "3.12"
         env:
             OS: ${{ matrix.os }}
             PYTHON: ${{ matrix.python }}
@@ -55,10 +59,10 @@ jobs:
         needs: test
         steps:
             - uses: actions/checkout@v2
-            - name: Set up Python 3.10
+            - name: Set up Python 3.12
               uses: actions/setup-python@v2
               with:
-                  python-version: "3.10"
+                  python-version: "3.12"
             - name: Install twine
               run: pip install twine
             - name: Install build dependencies

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/.github/workflows/release.yaml

@@ -18,6 +18,10 @@ jobs:
                 include:
                     - os: ubuntu-latest
                       python: "3.10"
+                    - os: ubuntu-latest
+                      python: "3.11"
+                    - os: ubuntu-latest
+                      python: "3.12"
         env:
             OS: ${{ matrix.os }}
             PYTHON: ${{ matrix.python }}
@@ -49,10 +53,10 @@ jobs:
         needs: test
         steps:
             - uses: actions/checkout@v2
-            - name: Set up Python 3.10
+            - name: Set up Python 3.12
               uses: actions/setup-python@v2
               with:
-                  python-version: "3.10"
+                  python-version: "3.12"
             - name: Install build dependencies
               run: python -m pip install --upgrade pip wheel twine build
             - name: Build package
@@ -68,10 +72,10 @@ jobs:
             - name: Checkout code
               uses: actions/checkout@v3
 
-            - name: Set up Python 3.10
+            - name: Set up Python 3.12
               uses: actions/setup-python@v4
               with:
-                  python-version: "3.10"
+                  python-version: "3.12"
 
             - name: Install hatch
               run: pip install hatch

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/.github/workflows/test.yaml

@@ -22,6 +22,10 @@ jobs:
                 include:
                     - os: ubuntu-latest
                       python: "3.10"
+                    - os: ubuntu-latest
+                      python: "3.11"
+                    - os: ubuntu-latest
+                      python: "3.12"
         env:
             OS: ${{ matrix.os }}
             PYTHON: ${{ matrix.python }}

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rectanglepy
-Version: 0.5.0
+Version: 0.5.2
 Summary: Hierarchical deconvolution of bulk  transcriptomics
 Project-URL: Documentation, https://rectanglepy.readthedocs.io/
 Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
@@ -36,6 +36,7 @@ Requires-Dist: numpy<2.0.0,>=1.0.0
 Requires-Dist: pydeseq2==0.4.11
 Requires-Dist: quadprog==0.1.12
 Requires-Dist: scipy==1.13.0
+Requires-Dist: setuptools<70.0.0,>=69.0.0
 Requires-Dist: statsmodels>=0.14.1
 Provides-Extra: dev
 Requires-Dist: bump2version; extra == 'dev'
@@ -64,10 +65,13 @@ Description-Content-Type: text/markdown
 [link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
 [badge-docs]: https://img.shields.io/readthedocs/rectanglepy
 
-Rectangle embodies a ”second-generation” deconvolution methodology, setting itself apart from other second-generation
-methods through its efficiency in signature creation and its handling of challenges within the deconvolution process.
-To establish a precise deconvolution method, we employ a hierarchical analysis approach, incorporate mRNA bias
-correction, and provide an estimation of unknown cellular content.
+Rectangle is an open-source Python package developed for computational deconvolution.
+
+Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical processing,
+an estimation of unknown cellular content and a significant reduction in data volume during signature matrix computation.
+
+Rectangle was developed to outperform existing deconvolution solutions by introducing methods that promise
+improvements in cell-type fraction estimation accuracy while keeping a low computational profile.
 
 ## Getting started
 
@@ -77,7 +81,7 @@ Please refer to the [documentation][link-docs]. In particular, the
 
 ## Installation
 
-You need to have Python 3.10 or newer installed on your system. If you don't have
+You need to have Python 3.10 or higher installed on your system. If you don't have
 Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 How to install Rectangle:

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/README.md

@@ -7,10 +7,13 @@
 [link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
 [badge-docs]: https://img.shields.io/readthedocs/rectanglepy
 
-Rectangle embodies a ”second-generation” deconvolution methodology, setting itself apart from other second-generation
-methods through its efficiency in signature creation and its handling of challenges within the deconvolution process.
-To establish a precise deconvolution method, we employ a hierarchical analysis approach, incorporate mRNA bias
-correction, and provide an estimation of unknown cellular content.
+Rectangle is an open-source Python package developed for computational deconvolution.
+
+Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical processing,
+an estimation of unknown cellular content and a significant reduction in data volume during signature matrix computation.
+
+Rectangle was developed to outperform existing deconvolution solutions by introducing methods that promise
+improvements in cell-type fraction estimation accuracy while keeping a low computational profile.
 
 ## Getting started
 
@@ -20,7 +23,7 @@ Please refer to the [documentation][link-docs]. In particular, the
 
 ## Installation
 
-You need to have Python 3.10 or newer installed on your system. If you don't have
+You need to have Python 3.10 or higher installed on your system. If you don't have
 Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 How to install Rectangle:

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/docs/conf.py

@@ -37,6 +37,8 @@ html_context = {
     "github_repo": "Rectangle",  # Repo name
     "github_version": "main",  # Version
     "conf_py_path": "/docs/",  # Path in the checkout to the docs root
+    "repository_url": repository_url,
+    "use_repository_button": True,
 }
 
 # -- General configuration ---------------------------------------------------
@@ -103,15 +105,29 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
+
 html_theme = "furo"
 html_static_path = ["_static"]
 html_title = "rectangle"
 
+
+html_logo = "_static/rec_logo.001.png"
+
 html_theme_options = {
-    "repository_url": repository_url,
-    "use_repository_button": True,
     "path_to_docs": "docs/",
+    "sidebar_hide_name": True,  # Hide the project name in the sidebar
+    "footer_icons": [
+        {
+            "name": "GitHub",
+            "url": repository_url,
+            "html": """
+                <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
+                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
+                </svg>
+            """,
+            "class": "",
+        },
+    ],
 }
 
 

rectanglepy-0.5.2/docs/notebooks/example.ipynb

@@ -0,0 +1,551 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example workflow"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "import rectanglepy as rectangle\n",
+    "from anndata import AnnData"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Load tutorial data"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "sc_counts, annotations, bulks  = rectangle.load_tutorial_data()"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "code",
+   "source": "sc_counts.iloc[:, :5].head()",
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T05:46:15.359490Z",
+     "start_time": "2025-01-23T05:46:15.352713Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "                       MIR1302-2HG  AL627309.1  AL627309.4  AC114498.1   \n",
+       "E2L4_GATGCTACAGGCACAA            0           0           0           0  \\\n",
+       "L5_AACAACCAGGAACTAT              0           0           0           0   \n",
+       "L5_TCCTTCTGTACTCCGG              0           0           0           0   \n",
+       "L2_GCCCGAACACGTATAC              0           0           0           0   \n",
+       "E2L2_ATGCATGTCACACCCT            0           0           0           0   \n",
+       "\n",
+       "                       AL669831.5  \n",
+       "E2L4_GATGCTACAGGCACAA           0  \n",
+       "L5_AACAACCAGGAACTAT             0  \n",
+       "L5_TCCTTCTGTACTCCGG             0  \n",
+       "L2_GCCCGAACACGTATAC             0  \n",
+       "E2L2_ATGCATGTCACACCCT           0  "
+      ],
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>MIR1302-2HG</th>\n",
+       "      <th>AL627309.1</th>\n",
+       "      <th>AL627309.4</th>\n",
+       "      <th>AC114498.1</th>\n",
+       "      <th>AL669831.5</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>E2L4_GATGCTACAGGCACAA</th>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>L5_AACAACCAGGAACTAT</th>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>L5_TCCTTCTGTACTCCGG</th>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>L2_GCCCGAACACGTATAC</th>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>E2L2_ATGCATGTCACACCCT</th>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "execution_count": 12
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "annotations.head()"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "code",
+   "source": "bulks.iloc[:, :5].head()",
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T05:46:13.242102Z",
+     "start_time": "2025-01-23T05:46:13.235377Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "         UBE2Q2P2  SSX9   CXorf67   EFCAB8  SPATA31B1P\n",
+       "pbmc_1   0.000000   0.0  0.118865  0.00000         0.0\n",
+       "pbmc_10  0.081115   0.0  0.086782  0.00000         0.0\n",
+       "pbmc_12  0.000000   0.0  0.188464  0.03157         0.0"
+      ],
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>UBE2Q2P2</th>\n",
+       "      <th>SSX9</th>\n",
+       "      <th>CXorf67</th>\n",
+       "      <th>EFCAB8</th>\n",
+       "      <th>SPATA31B1P</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>pbmc_1</th>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.118865</td>\n",
+       "      <td>0.00000</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>pbmc_10</th>\n",
+       "      <td>0.081115</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.086782</td>\n",
+       "      <td>0.00000</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>pbmc_12</th>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.188464</td>\n",
+       "      <td>0.03157</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "execution_count": 11
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Convert to AnnData object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "sc_adata = AnnData(sc_counts, obs=annotations.to_frame(name=\"cell_type\"))"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Single step Rectangle workflow"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "To deconvolute the bulk data in a single step, use the rectangle function. This function returns a tuple of the estimated cell type proportions and the signature result."
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "estimations, signature_result = rectangle.rectangle(sc_adata, bulks)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "code",
+   "source": "estimations",
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": "signature_result is a [`RectangleSignatureResult`](../generated/rectanglepy.pp.RectangleSignatureResult.rst) object.",
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# 2-step Rectangle workflow"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Rectangle can also be run in two steps, first creating the signature and then deconvoluting the bulk data."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Create Signature result"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "signature_result = rectangle.pp.build_rectangle_signatures(sc_adata, bulks=bulks)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "This creates a [`RectangleSignatureResult`](../generated/rectanglepy.pp.RectangleSignatureResult.rst) object."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Deconvolute bulk data"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "estimations = rectangle.tl.deconvolution(signature_result, bulks)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "This returns a pandas DataFrame with the estimated cell type proportions."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "source": "estimations.T",
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T05:46:46.255422Z",
+     "start_time": "2025-01-23T05:46:46.248810Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "                    pbmc_1       pbmc_10       pbmc_12\n",
+       "B cells           0.089947  1.099018e-01  7.147636e-02\n",
+       "ILC               0.008037  1.482882e-02  7.568929e-03\n",
+       "Monocytes         0.227473  2.967478e-01  2.255510e-01\n",
+       "NK cells          0.022183  1.626444e-02  1.011593e-01\n",
+       "Plasma cells      0.005894  6.567050e-04  3.095959e-03\n",
+       "Platelet          0.004847  2.190904e-02  1.863999e-02\n",
+       "T cells CD4 conv  0.037192 -6.450194e-18 -3.137140e-17\n",
+       "T cells CD8       0.161779  1.180941e-01  2.740643e-01\n",
+       "Tregs             0.416100  3.962703e-01  2.563935e-01\n",
+       "mDC               0.024173  2.066734e-02  1.005506e-02\n",
+       "pDC               0.002376  4.659653e-03  2.985398e-03\n",
+       "Unknown           0.000000  0.000000e+00  2.901021e-02"
+      ],
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>pbmc_1</th>\n",
+       "      <th>pbmc_10</th>\n",
+       "      <th>pbmc_12</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>B cells</th>\n",
+       "      <td>0.089947</td>\n",
+       "      <td>1.099018e-01</td>\n",
+       "      <td>7.147636e-02</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>ILC</th>\n",
+       "      <td>0.008037</td>\n",
+       "      <td>1.482882e-02</td>\n",
+       "      <td>7.568929e-03</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>Monocytes</th>\n",
+       "      <td>0.227473</td>\n",
+       "      <td>2.967478e-01</td>\n",
+       "      <td>2.255510e-01</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>NK cells</th>\n",
+       "      <td>0.022183</td>\n",
+       "      <td>1.626444e-02</td>\n",
+       "      <td>1.011593e-01</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>Plasma cells</th>\n",
+       "      <td>0.005894</td>\n",
+       "      <td>6.567050e-04</td>\n",
+       "      <td>3.095959e-03</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>Platelet</th>\n",
+       "      <td>0.004847</td>\n",
+       "      <td>2.190904e-02</td>\n",
+       "      <td>1.863999e-02</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>T cells CD4 conv</th>\n",
+       "      <td>0.037192</td>\n",
+       "      <td>-6.450194e-18</td>\n",
+       "      <td>-3.137140e-17</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>T cells CD8</th>\n",
+       "      <td>0.161779</td>\n",
+       "      <td>1.180941e-01</td>\n",
+       "      <td>2.740643e-01</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>Tregs</th>\n",
+       "      <td>0.416100</td>\n",
+       "      <td>3.962703e-01</td>\n",
+       "      <td>2.563935e-01</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>mDC</th>\n",
+       "      <td>0.024173</td>\n",
+       "      <td>2.066734e-02</td>\n",
+       "      <td>1.005506e-02</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>pDC</th>\n",
+       "      <td>0.002376</td>\n",
+       "      <td>4.659653e-03</td>\n",
+       "      <td>2.985398e-03</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>Unknown</th>\n",
+       "      <td>0.000000</td>\n",
+       "      <td>0.000000e+00</td>\n",
+       "      <td>2.901021e-02</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "execution_count": 14
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": ""
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3.9.12 ('squidpy39')",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "ae6466e8d4f517858789b5c9e8f0ed238fb8964458a36305fca7bddc149e9c64"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "rectanglepy"
-version = "0.5.0"
+version = "0.5.2"
 description = "Hierarchical deconvolution of bulk  transcriptomics"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -25,7 +25,8 @@ dependencies = [
     "loguru",
     "numpy>=1.0.0,<2.0.0",
     "anndata>=0.8.0,<0.10.9",
-    "statsmodels>=0.14.1"
+    "statsmodels>=0.14.1",
+    "setuptools>=69.0.0,<70.0.0",
 
 ]
 

{rectanglepy-0.5.0 → rectanglepy-0.5.2}/src/rectanglepy/pp/create_signature.py

@@ -172,6 +172,7 @@ def _create_bootstrap_signature(countsig, sc_data, annotations) -> pd.DataFrame:
     bootstrapped_signature = pd.DataFrame()
     number_of_bootstraps = 7
     samples_per_bootstrap = 500
+    np.random.seed(42)
     for celltype in celltypes:
         sc_data_filtered = sc_data.T[annotations == celltype]
         for i in range(number_of_bootstraps):
@@ -319,8 +320,10 @@ def build_rectangle_signatures(
     """
     annotations = adata.obs[cell_type_col]
     adata = adata[:, adata.X.sum(axis=0) > len(annotations.value_counts())]
+    assert adata.var_names.is_unique, "Duplicate gene found in adata"
 
     if bulks is not None:
+        assert bulks.columns.is_unique, "Duplicate gene found in bulks"
         genes = list(set(bulks.columns) & set(adata.var_names))
         genes = sorted(genes)
         assert len(genes) > 0, "No common genes between bulks and single-cell data"

rectanglepy-0.5.0/docs/notebooks/example.ipynb

@@ -1,324 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Example workflow"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "source": [],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-25T16:12:40.629887Z",
-     "start_time": "2024-03-25T16:12:39.074585Z"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "import rectanglepy as rectangle\n",
-    "from anndata import AnnData"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "## Load tutorial data"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-25T16:12:41.282874Z",
-     "start_time": "2024-03-25T16:12:40.630684Z"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "sc_counts, annotations, bulks  = rectangle.load_tutorial_data()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "outputs": [
-    {
-     "data": {
-      "text/plain": "                       MIR1302-2HG  AL627309.1  AL627309.4  AC114498.1   \nE2L4_GATGCTACAGGCACAA            0           0           0           0  \\\nL5_AACAACCAGGAACTAT              0           0           0           0   \nL5_TCCTTCTGTACTCCGG              0           0           0           0   \nL2_GCCCGAACACGTATAC              0           0           0           0   \nE2L2_ATGCATGTCACACCCT            0           0           0           0   \n\n                       AL669831.5  FAM41C  AL645608.5  NOC2L  PERM1  ISG15  \nE2L4_GATGCTACAGGCACAA           0       0           0      0      0      7  \nL5_AACAACCAGGAACTAT             0       0           0      0      0      1  \nL5_TCCTTCTGTACTCCGG             0       0           0      0      0      0  \nL2_GCCCGAACACGTATAC             0       0           0      0      0      2  \nE2L2_ATGCATGTCACACCCT           0       1           0      0      0      1  ",
-      "text/html": "<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>MIR1302-2HG</th>\n      <th>AL627309.1</th>\n      <th>AL627309.4</th>\n      <th>AC114498.1</th>\n      <th>AL669831.5</th>\n      <th>FAM41C</th>\n      <th>AL645608.5</th>\n      <th>NOC2L</th>\n      <th>PERM1</th>\n      <th>ISG15</th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>E2L4_GATGCTACAGGCACAA</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>7</td>\n    </tr>\n    <tr>\n      <th>L5_AACAACCAGGAACTAT</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>1</td>\n    </tr>\n    <tr>\n      <th>L5_TCCTTCTGTACTCCGG</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n    </tr>\n    <tr>\n      <th>L2_GCCCGAACACGTATAC</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>2</td>\n    </tr>\n    <tr>\n      <th>E2L2_ATGCATGTCACACCCT</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>1</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>1</td>\n    </tr>\n  </tbody>\n</table>\n</div>"
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "sc_counts.iloc[:, :10].head()"
-   ],
-   "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2024-03-25T16:12:41.300170Z",
-     "start_time": "2024-03-25T16:12:41.284686Z"
-    }
-   }
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "outputs": [
-    {
-     "data": {
-      "text/plain": "E2L4_GATGCTACAGGCACAA    Monocytes\nL5_AACAACCAGGAACTAT      Monocytes\nL5_TCCTTCTGTACTCCGG      Monocytes\nL2_GCCCGAACACGTATAC      Monocytes\nE2L2_ATGCATGTCACACCCT    Monocytes\nName: 0, dtype: object"
-     },
-     "execution_count": 4,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "annotations.head()"
-   ],
-   "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2024-03-25T16:12:41.982618Z",
-     "start_time": "2024-03-25T16:12:41.979126Z"
-    }
-   }
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "outputs": [
-    {
-     "data": {
-      "text/plain": "         UBE2Q2P2  SSX9   CXorf67   EFCAB8  SPATA31B1P  SDR16C6P     GTPBP6   \npbmc_1   0.000000   0.0  0.118865  0.00000         0.0       0.0  57.280197  \\\npbmc_10  0.081115   0.0  0.086782  0.00000         0.0       0.0  72.275326   \npbmc_12  0.000000   0.0  0.188464  0.03157         0.0       0.0  50.997427   \n\n          EFCAB12       A1BG  A1CF  \npbmc_1   0.252188  10.863071   0.0  \npbmc_10  0.095742  14.785649   0.0  \npbmc_12  0.100608   7.492537   0.0  ",
-      "text/html": "<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>UBE2Q2P2</th>\n      <th>SSX9</th>\n      <th>CXorf67</th>\n      <th>EFCAB8</th>\n      <th>SPATA31B1P</th>\n      <th>SDR16C6P</th>\n      <th>GTPBP6</th>\n      <th>EFCAB12</th>\n      <th>A1BG</th>\n      <th>A1CF</th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>pbmc_1</th>\n      <td>0.000000</td>\n      <td>0.0</td>\n      <td>0.118865</td>\n      <td>0.00000</td>\n      <td>0.0</td>\n      <td>0.0</td>\n      <td>57.280197</td>\n      <td>0.252188</td>\n      <td>10.863071</td>\n      <td>0.0</td>\n    </tr>\n    <tr>\n      <th>pbmc_10</th>\n      <td>0.081115</td>\n      <td>0.0</td>\n      <td>0.086782</td>\n      <td>0.00000</td>\n      <td>0.0</td>\n      <td>0.0</td>\n      <td>72.275326</td>\n      <td>0.095742</td>\n      <td>14.785649</td>\n      <td>0.0</td>\n    </tr>\n    <tr>\n      <th>pbmc_12</th>\n      <td>0.000000</td>\n      <td>0.0</td>\n      <td>0.188464</td>\n      <td>0.03157</td>\n      <td>0.0</td>\n      <td>0.0</td>\n      <td>50.997427</td>\n      <td>0.100608</td>\n      <td>7.492537</td>\n      <td>0.0</td>\n    </tr>\n  </tbody>\n</table>\n</div>"
-     },
-     "execution_count": 5,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "bulks.iloc[:, :10].head()"
-   ],
-   "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2024-03-25T16:12:43.131140Z",
-     "start_time": "2024-03-25T16:12:43.127235Z"
-    }
-   }
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Convert to AnnData object"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "outputs": [],
-   "source": [
-    "sc_adata = AnnData(sc_counts, obs=annotations.to_frame(name=\"cell_type\"))"
-   ],
-   "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2024-03-25T16:15:38.118620Z",
-     "start_time": "2024-03-25T16:15:38.098633Z"
-    }
-   }
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "# Single step Rectangle workflow"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "metadata": {},
-   "cell_type": "markdown",
-   "source": "To deconvolute the bulk data in a single step, use the rectangle function. This function returns a tuple of the estimated cell type proportions and the signature result."
-  },
-  {
-   "cell_type": "code",
-   "outputs": [],
-   "source": [
-    "estimations, signature_result = rectangle.rectangle(sc_adata, bulks)"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "execution_count": null
-  },
-  {
-   "cell_type": "code",
-   "outputs": [
-    {
-     "data": {
-      "text/plain": "          B cells       ILC  Monocytes  NK cells  Plasma cells  Platelet   \npbmc_1   0.075919  0.001291   0.279064  0.046658      0.010834  0.008950  \\\npbmc_10  0.093986  0.003410   0.316445  0.033528      0.002279  0.036153   \npbmc_12  0.060533  0.017572   0.251589  0.114043      0.002038  0.027041   \n\n         T cells CD4 conv  T cells CD8     Tregs       mDC       pDC   Unknown  \npbmc_1           0.139600     0.268706  0.069930  0.017415  0.001971  0.079661  \npbmc_10          0.243435     0.146063  0.011599  0.032518  0.005273  0.075309  \npbmc_12          0.119488     0.325029  0.024586  0.027099  0.004422  0.026560  ",
-      "text/html": "<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>B cells</th>\n      <th>ILC</th>\n      <th>Monocytes</th>\n      <th>NK cells</th>\n      <th>Plasma cells</th>\n      <th>Platelet</th>\n      <th>T cells CD4 conv</th>\n      <th>T cells CD8</th>\n      <th>Tregs</th>\n      <th>mDC</th>\n      <th>pDC</th>\n      <th>Unknown</th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>pbmc_1</th>\n      <td>0.075919</td>\n      <td>0.001291</td>\n      <td>0.279064</td>\n      <td>0.046658</td>\n      <td>0.010834</td>\n      <td>0.008950</td>\n      <td>0.139600</td>\n      <td>0.268706</td>\n      <td>0.069930</td>\n      <td>0.017415</td>\n      <td>0.001971</td>\n      <td>0.079661</td>\n    </tr>\n    <tr>\n      <th>pbmc_10</th>\n      <td>0.093986</td>\n      <td>0.003410</td>\n      <td>0.316445</td>\n      <td>0.033528</td>\n      <td>0.002279</td>\n      <td>0.036153</td>\n      <td>0.243435</td>\n      <td>0.146063</td>\n      <td>0.011599</td>\n      <td>0.032518</td>\n      <td>0.005273</td>\n      <td>0.075309</td>\n    </tr>\n    <tr>\n      <th>pbmc_12</th>\n      <td>0.060533</td>\n      <td>0.017572</td>\n      <td>0.251589</td>\n      <td>0.114043</td>\n      <td>0.002038</td>\n      <td>0.027041</td>\n      <td>0.119488</td>\n      <td>0.325029</td>\n      <td>0.024586</td>\n      <td>0.027099</td>\n      <td>0.004422</td>\n      <td>0.026560</td>\n    </tr>\n  </tbody>\n</table>\n</div>"
-     },
-     "execution_count": 9,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "estimations"
-   ],
-   "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2024-03-25T16:18:17.737030Z",
-     "start_time": "2024-03-25T16:18:17.731946Z"
-    }
-   },
-   "execution_count": 9
-  },
-  {
-   "cell_type": "markdown",
-   "source": "signature_result is a [`RectangleSignatureResult`](../generated/rectanglepy.pp.RectangleSignatureResult.rst) object.",
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "# 2-step Rectangle workflow"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "Rectangle can also be run in two steps, first creating the signature and then deconvoluting the bulk data."
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "## Create Signature result"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "outputs": [],
-   "source": [
-    "signature_result = rectangle.pp.build_rectangle_signatures(sc_adata, bulks=bulks)"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "This creates a [`RectangleSignatureResult`](../generated/rectanglepy.pp.RectangleSignatureResult.rst) object."
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "## Deconvolute bulk data"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "outputs": [],
-   "source": [
-    "estimations = rectangle.tl.deconvolution(signature_result, bulks)"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  },
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