CahanLab · pcahan1 · Feb 18, 2025 · Jun 27, 2024 · Sep 22, 2024 · Dec 17, 2024
diff --git a/docs/classifier.md b/docs/classifier.md
@@ -0,0 +1,7 @@
+# classifier functions
+
+more details on the clf object
+
+::: pySingleCellNet.classify
+
+
diff --git a/docs/img/logo.png b/docs/img/logo.png
diff --git a/docs/img/logoGlow.png b/docs/img/logoGlow.png
diff --git a/docs/index.md b/docs/index.md
@@ -0,0 +1,4 @@
+SingleCellNet predicts the _cell type_ of query scRNA-seq data by Random forest multi-class classification. See [Tan 2019](https://pubmed.ncbi.nlm.nih.gov/31377170/) for more details. It was [originally written in R](https://github.com/pcahan1/SingleCellNet). PySingleCellNet (**PySCN**) is the Python version, and it is compatible with [Scanpy](https://scanpy.readthedocs.io/en/stable/). PySCN was crafted to aid in the analysis of engineered cell populations (i.e. cells derived via directed differentiation of pluripotent stem cells or via direct conversion), but can just as easily be used to perform _cell typing_ on data dervived from other sources as long as adequate training data is available.
+
+
+
diff --git a/docs/install.md b/docs/install.md
@@ -0,0 +1,14 @@
+PySingleCellnet depends on several packages, most of which can be installed with pip, and some are available in conda channels.
+
+### Prerequisites
+
+```python
+pip install pandas numpy sklearn scanpy statsmodels scipy matplotlib seaborn umap-learn
+```
+
+### Installation
+
+```python
+!pip install git+https://github.com/pcahan1/PySingleCellNet/
+```
+
diff --git a/docs/javascripts/extra.js b/docs/javascripts/extra.js
@@ -0,0 +1,10 @@
+// Using the document$ observable from mkdocs-material to get notified of page "reload" also if using `navigation.instant` (SSA)
+document$.subscribe(function() {
+  // First check if the page contains a notebook-related class
+  if (document.querySelector('.jp-Notebook')) {
+    document.querySelector("div.md-sidebar.md-sidebar--secondary").remove();
+ //   document.querySelector("div.md-sidebar.md-sidebar--primary").remove();
+  }
+});
+
+
diff --git a/docs/notebooks/Basics.ipynb b/docs/notebooks/Basics.ipynb
diff --git a/docs/notebooks/categorize.ipynb b/docs/notebooks/categorize.ipynb
diff --git a/docs/notebooks/eb_diagram.png b/docs/notebooks/eb_diagram.png
diff --git a/docs/source/notebooks/enrichment.ipynb → docs/notebooks/enrichment.ipynb b/docs/source/notebooks/enrichment.ipynb → docs/notebooks/enrichment.ipynb
diff --git a/docs/source/notebooks/explore.ipynb → docs/notebooks/explore.ipynb b/docs/source/notebooks/explore.ipynb → docs/notebooks/explore.ipynb
diff --git a/...books/how-to_prepare_reference_data.ipynb → ...books/how-to_prepare_reference_data.ipynb b/...books/how-to_prepare_reference_data.ipynb → ...books/how-to_prepare_reference_data.ipynb
diff --git a/docs/notebooks/img/categories.jpg b/docs/notebooks/img/categories.jpg
diff --git a/docs/notebooks/img/eb_diagram.png b/docs/notebooks/img/eb_diagram.png
diff --git a/docs/notebooks/old_quickstart.ipynb b/docs/notebooks/old_quickstart.ipynb
diff --git a/docs/notebooks/quickstart.ipynb b/docs/notebooks/quickstart.ipynb
diff --git a/docs/source/notebooks/train_classifier.ipynb → docs/notebooks/train_classifier.ipynb b/docs/source/notebooks/train_classifier.ipynb → docs/notebooks/train_classifier.ipynb
diff --git a/docs/plotting.md b/docs/plotting.md
@@ -0,0 +1,4 @@
+# plotting functions
+
+::: pySingleCellNet.plotting
+
diff --git a/docs/source/refs.md → docs/refs.md b/docs/source/refs.md → docs/refs.md
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/source/apidocs/index.md b/docs/source/apidocs/index.md
diff --git a/docs/source/conf.py b/docs/source/conf.py
diff --git a/docs/source/install.md b/docs/source/install.md
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
@@ -0,0 +1,9 @@
+/* hide jupyter notebooks input/output numbers */
+.jp-InputPrompt {
+  display: none !important;
+}
+
+.jp-OutputPrompt {
+  display: none !important;
+}
+
diff --git a/docs/source/training_data.md → docs/training_data.md b/docs/source/training_data.md → docs/training_data.md
diff --git a/docs/utils.md b/docs/utils.md
@@ -0,0 +1,6 @@
+# utility functions
+
+Add a brief summary here
+
+::: pySingleCellNet.utils
+
diff --git a/md_img/HM_Lung_Leiden_101120.png b/md_img/HM_Lung_Leiden_101120.png
diff --git a/md_img/HM_Val_Lung_100920.png b/md_img/HM_Val_Lung_100920.png
diff --git a/md_img/HM_Val_Other_100920.png b/md_img/HM_Val_Other_100920.png
diff --git a/md_img/HM_Val_Other_softmax_100920.png b/md_img/HM_Val_Other_softmax_100920.png
diff --git a/md_img/PR_curves_Lung_100920.png b/md_img/PR_curves_Lung_100920.png
diff --git a/md_img/UMAP_Lung_Other_101120.png b/md_img/UMAP_Lung_Other_101120.png
diff --git a/md_img/UMAP_Lung_SCN_101120.png b/md_img/UMAP_Lung_SCN_101120.png
diff --git a/md_img/hm_mgenes_result.png b/md_img/hm_mgenes_result.png
diff --git a/md_img/output_17_0.png b/md_img/output_17_0.png
diff --git a/md_img/output_18_0.png b/md_img/output_18_0.png
diff --git a/md_img/output_20_0.png b/md_img/output_20_0.png
diff --git a/md_img/output_21_0.png b/md_img/output_21_0.png
diff --git a/md_img/output_22_0.png b/md_img/output_22_0.png
diff --git a/md_img/output_24_0.png b/md_img/output_24_0.png
diff --git a/md_img/pca_lung_101120.png b/md_img/pca_lung_101120.png
diff --git a/md_img/temp b/md_img/temp
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -0,0 +1,77 @@
+site_name: pySingleCellNet
+site_author: Patrick Cahan
+copyright: Copyright &copy; 2024 Cahan Lab
+repo_url: https://github.com/CahanLab/PySingleCellNet
+
+use_directory_urls: false
+
+extra_css:
+  - stylesheets/extra.css
+
+extra_javascript:
+  - javascripts/extra.js
+
+theme:
+  name: material
+  font:
+    text: Noto Sans
+  palette:
+    primary: light blue
+  logo: img/logoGlow.png
+  favicon: img/logo.png
+  features:
+    - content.footnote.tooltips
+    - navigation.expand
+    - toc.integrate
+#    - navigation.tabs
+#    - navigation.tabs.sticky
+#    - navigation.sections
+
+markdown_extensions:
+  - md_in_html
+  - footnotes
+  - admonition
+  - attr_list
+  - tables
+  - def_list
+  - toc:
+      title: On this page
+  - pymdownx.blocks.caption
+  - pymdownx.tasklist:
+      custom_checkbox: false
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+
+plugins:
+  - mkdocstrings:
+      handlers:
+        python:
+          options:
+            separate_signature: true
+            docstring_section_style: list
+            heading_level: 3
+  - search
+  - mkdocs-jupyter:
+      execute: false
+      include_source: True
+
+nav:
+#  - Home: index.md
+  - Installation: install.md
+  - Tutorials: 
+    - 'Quickstart': notebooks/quickstart.ipynb
+    - 'Explore': notebooks/categorize.ipynb
+#    - 'train & classify': 'notebooks/Basics.ipynb'
+#    - 'analyze _in vitro_ cells': 'notebooks/explore.ipynb'
+#    - 'prepare training data': 'notebooks/how-to_prepare_reference_data.ipynb'
+#    - 'Train a classifier': 'notebooks/train_classifier.ipynb'
+#    - 'Enrichment analysis': 'notebooks/enrichment.ipynb'
+  - Training data: training_data.md
+  - References: refs.md
+  - API:
+    - 'Utility functions': 'utils.md'
+    - 'Classifier functions': 'classifier.md'
+    - 'Plotting functions': 'plotting.md'
+
+
diff --git a/docs/Makefile → old_docs/Makefile b/docs/Makefile → old_docs/Makefile
diff --git a/docs/make.bat → old_docs/make.bat b/docs/make.bat → old_docs/make.bat
diff --git a/old_docs/requirements.txt b/old_docs/requirements.txt
@@ -0,0 +1,8 @@
+sphinx
+sphinx-rtd-theme
+sphinx-autodoc-typehints
+sphinxcontrib-napoleon
+nbsphinx
+myst-nb
+sphinx-copybutton
+sphinx-book-theme
diff --git a/docs/source/SCN_refs.bib → old_docs/source/SCN_refs.bib b/docs/source/SCN_refs.bib → old_docs/source/SCN_refs.bib
diff --git a/docs/source/_static/pySCN.png → old_docs/source/_static/pySCN.png b/docs/source/_static/pySCN.png → old_docs/source/_static/pySCN.png
diff --git a/docs/source/_static/pySCN_tree.png → old_docs/source/_static/pySCN_tree.png b/docs/source/_static/pySCN_tree.png → old_docs/source/_static/pySCN_tree.png
diff --git a/old_docs/source/apidocs/modules.rst b/old_docs/source/apidocs/modules.rst
@@ -0,0 +1,7 @@
+pySingleCellNet
+===============
+
+.. toctree::
+   :maxdepth: 4
+
+   pySingleCellNet
diff --git a/old_docs/source/apidocs/pySingleCellNet.config.rst b/old_docs/source/apidocs/pySingleCellNet.config.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.config
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.plotting.bar.rst b/old_docs/source/apidocs/pySingleCellNet.plotting.bar.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.plotting.bar
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.plotting.dot.rst b/old_docs/source/apidocs/pySingleCellNet.plotting.dot.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.plotting.dot
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.plotting.heatmap.rst b/old_docs/source/apidocs/pySingleCellNet.plotting.heatmap.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.plotting.heatmap
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.plotting.rst b/old_docs/source/apidocs/pySingleCellNet.plotting.rst
@@ -0,0 +1,18 @@
+pySingleCellNet.plotting package
+================================
+
+.. automodule:: pySingleCellNet.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pySingleCellNet.plotting.bar
+   pySingleCellNet.plotting.dot
+   pySingleCellNet.plotting.heatmap
+   pySingleCellNet.plotting.scatter
diff --git a/old_docs/source/apidocs/pySingleCellNet.plotting.scatter.rst b/old_docs/source/apidocs/pySingleCellNet.plotting.scatter.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.plotting.scatter
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.postclass_analysis.rst b/old_docs/source/apidocs/pySingleCellNet.postclass_analysis.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.postclass_analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.rank_class.rst b/old_docs/source/apidocs/pySingleCellNet.rank_class.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.rank_class
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.rst b/old_docs/source/apidocs/pySingleCellNet.rst
@@ -0,0 +1,30 @@
+pySingleCellNet package
+=======================
+
+.. automodule:: pySingleCellNet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pySingleCellNet.plotting
+   pySingleCellNet.utils
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pySingleCellNet.config
+   pySingleCellNet.postclass_analysis
+   pySingleCellNet.rank_class
+   pySingleCellNet.scn_assess
+   pySingleCellNet.scn_train
+   pySingleCellNet.stats
+   pySingleCellNet.tsp_rf
diff --git a/old_docs/source/apidocs/pySingleCellNet.scn_assess.rst b/old_docs/source/apidocs/pySingleCellNet.scn_assess.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.scn_assess
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.scn_train.rst b/old_docs/source/apidocs/pySingleCellNet.scn_train.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.scn_train
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.stats.rst b/old_docs/source/apidocs/pySingleCellNet.stats.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.stats
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.tsp_rf.rst b/old_docs/source/apidocs/pySingleCellNet.tsp_rf.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.tsp_rf
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.utils.adataTools.rst b/old_docs/source/apidocs/pySingleCellNet.utils.adataTools.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.utils.adataTools
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.utils.annotation.rst b/old_docs/source/apidocs/pySingleCellNet.utils.annotation.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.utils.annotation
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.utils.colors.rst b/old_docs/source/apidocs/pySingleCellNet.utils.colors.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.utils.colors
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.utils.oldFunctions.rst b/old_docs/source/apidocs/pySingleCellNet.utils.oldFunctions.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.utils.oldFunctions
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.utils.qc.rst b/old_docs/source/apidocs/pySingleCellNet.utils.qc.rst
@@ -0,0 +1,4 @@
+.. automodule:: pySingleCellNet.utils.qc
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/old_docs/source/apidocs/pySingleCellNet.utils.rst b/old_docs/source/apidocs/pySingleCellNet.utils.rst
@@ -0,0 +1,19 @@
+pySingleCellNet.utils package
+=============================
+
+.. automodule:: pySingleCellNet.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pySingleCellNet.utils.adataTools
+   pySingleCellNet.utils.annotation
+   pySingleCellNet.utils.colors
+   pySingleCellNet.utils.oldFunctions
+   pySingleCellNet.utils.qc
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,4 @@
		SingleCellNet predicts the _cell type_ of query scRNA-seq data by Random forest multi-class classification. See [Tan 2019](https://pubmed.ncbi.nlm.nih.gov/31377170/) for more details. It was [originally written in R](https://github.com/pcahan1/SingleCellNet). PySingleCellNet (PySCN) is the Python version, and it is compatible with [Scanpy](https://scanpy.readthedocs.io/en/stable/). PySCN was crafted to aid in the analysis of engineered cell populations (i.e. cells derived via directed differentiation of pluripotent stem cells or via direct conversion), but can just as easily be used to perform _cell typing_ on data dervived from other sources as long as adequate training data is available.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,4 @@
		# plotting functions

		::: pySingleCellNet.plotting