4-umap.py

# Define UMAP
brain_umap = umap.UMAP(random_state=999, n_neighbors=30, min_dist=.25)

# Fit UMAP and extract latent vars 1-2
embedding = pd.DataFrame(brain_umap.fit_transform(matrix), columns = ['UMAP1','UMAP2'])

# Produce sns.scatterplot and pass metadata.subclasses as color
sns_plot = sns.scatterplot(x='UMAP1', y='UMAP2', data=embedding,
                hue=metadata.subclass_label.to_list(),
                alpha=.1, linewidth=0, s=1)
# Adjust legend
sns_plot.legend(loc='center left', bbox_to_anchor=(1, .5))
# Save PNG
sns_plot.figure.savefig('umap_scatter.png', bbox_inches='tight', dpi=500)