Functional analysis (icbi-lab#6)

* Initial commit for functional analysis# * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add plotting utils * add utils * Paths and Data loading * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added first calls for deseq2-py analysis and progeny * WIP: cleanup, finalize barplots and heatmap * WIP: cleanup, added target_plot for significant pathways * WIP: dorothea analysis * dorothea analysis: make TF panels with volcano plots * MSigDB ORA analysis: add MSigDB overrepresentation analysis * WIP: CytoSig * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * precommit activated * included notebook in toctree * added functions to api.md * fix intersphinx conf * fix intersphinx conf * Added CytoSig analysis * Added MSigDB OAR barplots and volcano plots. Doc * Save MSigDB and CytoSig result tables as tsv * Doc * Add references * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix __init__ * fix api.md * Restrict number of barplots in notebook. Switch to GSEA for MSigDB * Remove empty cell * Fix typo * Be verbose about supressed output. Display path to results after storing plots. * Switch to R generated DESeq2 results from differential_despression. Doc. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Numbering * Clean up * Update text functional analysis * Cleanup, use with plt.ioff():, auto determine plot provider for saving plots --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gregor Sturm <[email protected]>
vjmarteau · Apr 25, 2023 · 20dace7 · 20dace7
1 parent 9b13cda
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diff --git a/.gitignore b/.gitignore
@@ -30,4 +30,7 @@ __pycache__/
 # IDEs
 /.idea/
 /.vscode/
+
+# remote kernel files
+rik_kernel-*
 .ipynb_checkpoints
diff --git a/docs/api.md b/docs/api.md
@@ -49,6 +49,8 @@
 .. autosummary::
     :toctree: generated
 
+    pl.reshape_clustermap
+    pl.save_fig_mfmt
     pl.significance_heatmap
     pl.plot_paired
 ```
diff --git a/docs/conf.py b/docs/conf.py
@@ -96,6 +96,7 @@
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "sccoda": ("https://sccoda.readthedocs.io/en/latest/", None),
+    "seaborn": ("https://seaborn.pydata.org/", None),
     "pandas": ("https://pandas.pydata.org/docs/", None),
     "scanpy": ("https://scanpy.readthedocs.io/en/stable", None),
 }
@@ -128,6 +129,7 @@
     # If building the documentation fails because of a missing link that is outside your control,
     # you can add an exception to this list.
     #     ("py:class", "igraph.Graph"),
+    ("py:class", "seaborn.matrix.ClusterGrid"),
 ]
 
 

diff --git a/docs/index.md b/docs/index.md
@@ -28,6 +28,7 @@ notebooks/05_cell_type_annotation.ipynb
 
 notebooks/06_differential_expression.ipynb
 notebooks/09_compositional.ipynb
+notebooks/10_functional_analysis.ipynb
 notebooks/15_cell_cell_communication.ipynb
 notebooks/10_bulk_integration.ipynb
 

diff --git a/docs/notebooks/06_differential_expression.ipynb b/docs/notebooks/06_differential_expression.ipynb
@@ -5,6 +5,7 @@
    "id": "07fb6109-7a52-4379-8655-9d2d2f3a7388",
    "metadata": {},
    "source": [
+    "(differential_expression)=\n",
     "# Differential gene expression\n",
     "\n",
     "One of the most commonly asked questions when comparing between conditions is which genes\n",

diff --git a/docs/notebooks/06_differential_expression.py b/docs/notebooks/06_differential_expression.py
@@ -13,6 +13,7 @@
 # ---
 
 # %% [markdown]
+# (differential_expression)=
 # # Differential gene expression
 #
 # One of the most commonly asked questions when comparing between conditions is which genes