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jkobject committed Dec 30, 2023
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22 changes: 15 additions & 7 deletions dataset/index.html
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Expand Up @@ -234,10 +234,7 @@ <h3 id="scdataloader.data.Dataset.use_prior_network" class="doc doc-heading">
</table>
<details class="quote">
<summary>Source code in <code>scdataloader/data.py</code></summary>
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Expand Down Expand Up @@ -266,7 +263,14 @@ <h3 id="scdataloader.data.Dataset.use_prior_network" class="doc doc-heading">
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<span class="normal">201</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">use_prior_network</span><span class="p">(</span>
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<span class="normal">208</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">use_prior_network</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;collectri&quot;</span><span class="p">,</span> <span class="n">organism</span><span class="o">=</span><span class="s2">&quot;human&quot;</span><span class="p">,</span> <span class="n">split_complexes</span><span class="o">=</span><span class="kc">True</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
Expand All @@ -284,15 +288,19 @@ <h3 id="scdataloader.data.Dataset.use_prior_network" class="doc doc-heading">
<span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;tflink&quot;</span><span class="p">:</span>
<span class="n">TFLINK</span> <span class="o">=</span> <span class="s2">&quot;https://cdn.netbiol.org/tflink/download_files/TFLink_Homo_sapiens_interactions_All_simpleFormat_v1.0.tsv.gz&quot;</span>
<span class="n">net</span> <span class="o">=</span> <span class="n">pd_load_cached</span><span class="p">(</span><span class="n">TFLINK</span><span class="p">)</span>
<span class="n">net</span> <span class="o">=</span> <span class="n">net</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;Name.TF&quot;</span><span class="p">:</span> <span class="s2">&quot;regulator&quot;</span><span class="p">,</span> <span class="s2">&quot;Name.Target&quot;</span><span class="p">:</span> <span class="s2">&quot;target&quot;</span><span class="p">})</span>
<span class="n">net</span> <span class="o">=</span> <span class="n">net</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span>
<span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;Name.TF&quot;</span><span class="p">:</span> <span class="s2">&quot;regulator&quot;</span><span class="p">,</span> <span class="s2">&quot;Name.Target&quot;</span><span class="p">:</span> <span class="s2">&quot;target&quot;</span><span class="p">}</span>
<span class="p">)</span>
<span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;htftarget&quot;</span><span class="p">:</span>
<span class="n">HTFTARGET</span> <span class="o">=</span> <span class="s2">&quot;http://bioinfo.life.hust.edu.cn/static/hTFtarget/file_download/tf-target-infomation.txt&quot;</span>
<span class="n">net</span> <span class="o">=</span> <span class="n">pd_load_cached</span><span class="p">(</span><span class="n">HTFTARGET</span><span class="p">)</span>
<span class="n">net</span> <span class="o">=</span> <span class="n">net</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;TF&quot;</span><span class="p">:</span> <span class="s2">&quot;regulator&quot;</span><span class="p">})</span>
<span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;collectri&quot;</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">decoupler</span> <span class="k">as</span> <span class="nn">dc</span>

<span class="n">net</span> <span class="o">=</span> <span class="n">dc</span><span class="o">.</span><span class="n">get_collectri</span><span class="p">(</span><span class="n">organism</span><span class="o">=</span><span class="n">organism</span><span class="p">,</span> <span class="n">split_complexes</span><span class="o">=</span><span class="n">split_complexes</span><span class="p">)</span>
<span class="n">net</span> <span class="o">=</span> <span class="n">dc</span><span class="o">.</span><span class="n">get_collectri</span><span class="p">(</span>
<span class="n">organism</span><span class="o">=</span><span class="n">organism</span><span class="p">,</span> <span class="n">split_complexes</span><span class="o">=</span><span class="n">split_complexes</span>
<span class="p">)</span>
<span class="n">net</span> <span class="o">=</span> <span class="n">net</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;source&quot;</span><span class="p">:</span> <span class="s2">&quot;regulator&quot;</span><span class="p">})</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
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48 changes: 33 additions & 15 deletions index.html
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Expand Up @@ -43,9 +43,11 @@
<ul class="current">
<li class="toctree-l1 current"><a class="reference internal current" href=".">Home</a>
<ul class="current">
<li class="toctree-l2"><a class="reference internal" href="#commands">Commands</a>
<li class="toctree-l2"><a class="reference internal" href="#install-it-from-pypi">Install it from PyPI</a>
</li>
<li class="toctree-l2"><a class="reference internal" href="#project-layout">Project layout</a>
<li class="toctree-l2"><a class="reference internal" href="#usage">Usage</a>
</li>
<li class="toctree-l2"><a class="reference internal" href="#development">Development</a>
</li>
</ul>
</li>
Expand Down Expand Up @@ -89,21 +91,37 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div class="section" itemprop="articleBody">

<h1 id="welcome-to-mkdocs">Welcome to MkDocs</h1>
<p>For full documentation visit <a href="https://www.mkdocs.org">mkdocs.org</a>.</p>
<h2 id="commands">Commands</h2>
<h1 id="scdataloader">scdataloader</h1>
<p><a href="https://codecov.io/gh/jkobject/scDataLoader"><img alt="codecov" src="https://codecov.io/gh/jkobject/scDataLoader/branch/main/graph/badge.svg?token=scDataLoader_token_here" /></a>
<a href="https://github.com/jkobject/scDataLoader/actions/workflows/main.yml"><img alt="CI" src="https://github.com/jkobject/scDataLoader/actions/workflows/main.yml/badge.svg" /></a></p>
<p>Awesome single cell dataloader created by @jkobject</p>
<p>This data loader is designed to be used with:</p>
<ul>
<li><a href="https://lamin.ai/">lamindb</a></li>
</ul>
<p>and:</p>
<ul>
<li><code>mkdocs new [dir-name]</code> - Create a new project.</li>
<li><code>mkdocs serve</code> - Start the live-reloading docs server.</li>
<li><code>mkdocs build</code> - Build the documentation site.</li>
<li><code>mkdocs -h</code> - Print help message and exit.</li>
<li><a href="https://scanpy.readthedocs.io/en/stable/">scanpy</a></li>
<li><a href="https://anndata.readthedocs.io/en/latest/">anndata</a></li>
</ul>
<h2 id="project-layout">Project layout</h2>
<pre><code>mkdocs.yml # The configuration file.
docs/
index.md # The documentation homepage.
... # Other markdown pages, images and other files.
<p>It allows you to:</p>
<ol>
<li>load thousands of datasets containing millions of cells in a few seconds.</li>
<li>preprocess the data per dataset and download it locally (normalization, filtering, etc.)</li>
<li>create a more complex single cell dataset</li>
<li>extend it to your need</li>
</ol>
<h2 id="install-it-from-pypi">Install it from PyPI</h2>
<pre><code class="language-bash">pip install scdataloader
</code></pre>
<h2 id="usage">Usage</h2>
<p>see the notebooks in <a href="https://jkobject.github.io/scDataLoader/">docs</a>:</p>
<ol>
<li><a href="https://jkobject.github.io/scDataLoader/notebooks/01_load_dataset.html">load a dataset</a></li>
<li><a href="https://jkobject.github.io/scDataLoader/notebooks/02_create_dataset.html">create a dataset</a></li>
</ol>
<h2 id="development">Development</h2>
<p>Read the <a href="CONTRIBUTING.md">CONTRIBUTING.md</a> file.</p>

</div>
</div><footer>
Expand Down Expand Up @@ -152,5 +170,5 @@ <h2 id="project-layout">Project layout</h2>

<!--
MkDocs version : 1.5.3
Build Date UTC : 2023-12-30 13:48:46.007737+00:00
Build Date UTC : 2023-12-30 14:36:39.696726+00:00
-->
46 changes: 34 additions & 12 deletions index.md
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@@ -1,17 +1,39 @@
# Welcome to MkDocs
# scdataloader

For full documentation visit [mkdocs.org](https://www.mkdocs.org).
[![codecov](https://codecov.io/gh/jkobject/scDataLoader/branch/main/graph/badge.svg?token=scDataLoader_token_here)](https://codecov.io/gh/jkobject/scDataLoader)
[![CI](https://github.com/jkobject/scDataLoader/actions/workflows/main.yml/badge.svg)](https://github.com/jkobject/scDataLoader/actions/workflows/main.yml)

## Commands
Awesome single cell dataloader created by @jkobject

* `mkdocs new [dir-name]` - Create a new project.
* `mkdocs serve` - Start the live-reloading docs server.
* `mkdocs build` - Build the documentation site.
* `mkdocs -h` - Print help message and exit.
This data loader is designed to be used with:

## Project layout
- [lamindb](https://lamin.ai/)

mkdocs.yml # The configuration file.
docs/
index.md # The documentation homepage.
... # Other markdown pages, images and other files.
and:

- [scanpy](https://scanpy.readthedocs.io/en/stable/)
- [anndata](https://anndata.readthedocs.io/en/latest/)

It allows you to:

1. load thousands of datasets containing millions of cells in a few seconds.
2. preprocess the data per dataset and download it locally (normalization, filtering, etc.)
3. create a more complex single cell dataset
4. extend it to your need

## Install it from PyPI

```bash
pip install scdataloader
```

## Usage

see the notebooks in [docs](https://jkobject.github.io/scDataLoader/):

1. [load a dataset](https://jkobject.github.io/scDataLoader/notebooks/01_load_dataset.html)
2. [create a dataset](https://jkobject.github.io/scDataLoader/notebooks/02_create_dataset.html)

## Development

Read the [CONTRIBUTING.md](CONTRIBUTING.md) file.
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12 changes: 6 additions & 6 deletions preprocess/index.html
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Expand Up @@ -220,7 +220,8 @@ <h2 id="scdataloader.preprocess.Preprocessor" class="doc doc-heading">
</table>
<details class="quote">
<summary>Source code in <code>scdataloader/preprocess.py</code></summary>
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<span class="bp">self</span><span class="p">,</span>
<span class="n">lb</span><span class="p">,</span>
<span class="n">filter_gene_by_counts</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">bool</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
Expand Down Expand Up @@ -425,7 +425,8 @@ <h3 id="scdataloader.preprocess.Preprocessor.__call__" class="doc doc-heading">
</table>
<details class="quote">
<summary>Source code in <code>scdataloader/preprocess.py</code></summary>
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<span class="normal">164</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">data</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">ln</span><span class="o">.</span><span class="n">Dataset</span><span class="p">,</span> <span class="n">AnnData</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">name</span><span class="o">=</span><span class="s2">&quot;preprocessed dataset&quot;</span><span class="p">,</span>
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