hello-clusters sweep notebook #982
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Ready for review, now using the Docker image in CI! |
jashapiro
approved these changes
Jan 14, 2025
| * `resolution`: The resolution parameter (1; used only with Louvain and Leiden clustering) | ||
| * `objective_function`: The objective function to optimize clusters (CPM; used only with Leiden clustering) | ||
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| `rOpenScPCA::sweep_clusters()` does allow you to specify values for any other parameters. |
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I'm not sure what you are trying to say here? Can you clarify this?
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I was in fact trying to say "doesn't", which is a rather different interpretation!
| # Plot the UMAP, colored by the new cluster variable | ||
| ggplot(umap_df_plot, aes(x = UMAP1, y = UMAP2, color = cluster)) + | ||
| geom_point(alpha = 0.6) + | ||
| labs(title = glue::glue("nearest neighbors: {clustering_name}")) + |
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I had a thought that you might instead show this by getting the value from the table rather than the list name, but either way is fine. I might say when you name the list that you will use it for labeling plots, rather than just saying it is optional.
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Update, I see you do this later, so I think it is fine to show both ways. I'd still add the comment when you add the names though!
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
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Closes #797
This PR adds the next
hello-clustersnotebook to sweep parameters.In the first section, I sweep across
nn=seq(10,30,10), plot UMAPs, and calculate & plot metrics with a brief sentence interpreting. In the second section, I sweep acrossnn=seq(10,30,10)andres=seq(5,15,5)/10and show code to assess the results but I do not interpret. Currently I don't export anything. It didn't seem to me that anything was super necessary to export to communicate the main notebook points, but I suppose we can export a TSV or PNG or so if something is really wanted.I also updated the module README and added this next notebook to the module bash script.
Please let me know where I can expand, shorten, or reframe! Here's the notebook:
02_compare-clustering-parameters.nb.html.zip