Added working example for scmodule

notebooks/example.py

@@ -0,0 +1,85 @@
+#!usr/bin/python
+"""Example code for using scmodule part of the library."""
+# ---------------------------------------------------------------------
+# Example - compute co-expression modules using a scanpy anndata object
+# Updated: 04/08/24
+# ---------------------------------------------------------------------
+import logging
+import os
+import scdemon as sm
+import scanpy as sc
+import numpy as np
+from scdemon.auxiliary import recipe_full
+
+# Set logging level:
+logging.basicConfig(level=logging.INFO)
+
+
+# Load and prep datasets:
+# -----------------------
+# Or one of scanpy's datasets:
+tag = "pbmc_example"
+annfile = tag + "_ann.h5ad"
+if os.path.exists(annfile):
+    adata = sc.read(annfile)
+else:
+    adata = sc.datasets.pbmc3k()
+    recipe_full(adata, preprocess=True, annotate=True)
+    adata.write(annfile)
+
+logging.info("Loaded example dataset")
+
+# Set arguments for plotting outputs:
+imgdir = "./"
+# Make the scmodule object:
+max_k = 100
+mod = sm.scmodule(adata,
+                  # Where files+plots go / what they are called:
+                  csuff=tag, imgdir=imgdir,
+                  # Options for graph creation:
+                  estimate_sd=False,
+                  svd_k=max_k, filter_expr=0.05, z=4.5,
+                  # Overall usage/correlation computation options:
+                  calc_raw=False)
+mod.setup()  # Setup the object
+
+
+# Make graph using the selected parameters for basic analysis:
+# ------------------------------------------------------------
+graph_id = "base"
+mod.make_graph(graph_id, resolution=2.5)
+mod.plot_graph(graph_id, attr="leiden", show_labels=True, width=16)
+mod.plot_gene_umap(graph_id, attr="leiden", width=16)
+
+# Modules on cell UMAP:
+mod.plot_umap_grid(graph_id)
+
+# Get the modules/print out:
+mlist = mod.get_modules(graph_id, print_modules=False)
+mod.save_modules(graph_id)
+
+# Get functional enrichments for the modules:
+gpres = mod.get_goterms(graph_id)
+
+
+# We can plot additional plots on the gene modules graph or UMAP:
+# ---------------------------------------------------------------
+# Plot the logFC for a specific covariate on the graph:
+graph_id = "base"
+covariate = "leiden"
+mod.plot_gene_logfc(graph_id, attr=covariate,
+                    show_labels=False, width=16, fc_cut=2)
+
+# Plot correlation of SVD components with covariates:
+cvlist = ["n_genes", "leiden"]
+mod.plot_svd_corr(cvlist)
+
+# Plot the average expression of leiden modules on covariates:
+mod.plot_heatmap_avgexpr(graph_id, cvlist=cvlist, attr="leiden")
+
+# Make a graph from only specific SVD covariate-correlated components
+# Such as components correlated with celltypes:
+mod.make_subset_graph(graph_id, "leiden", cv_cutoff=2.0)
+mod.plot_graph(graph_id + "_cls", attr="leiden", show_labels=True, width=16)
+mod.plot_heatmap_avgexpr(graph_id, cvlist=['leiden'], attr="leiden")
+mod.plot_umap_grid(graph_id)