Generate similar escape plots and UMAP analysis for data from previous Perth09 studies, plus some cleanup of current HK/19 DMS plots. Addresses the following points from @jbloom:
HongKong/2019
Remove 3-month-old infant 2462 from list of pedatric samples, and plot separately. Notebook and figures in scratch_notebooks/figure_drafts/sitewise_escape/.
Perth09
Generate sitewise escape plots for selected sites. These are found in scratch_notebooks/figure_drafts/perth09_analysis.
Note that Perth09 data needs to be renumbered before I can make a full-protein plot. Currently uses format (HA2)1 etc. for sites in HA2, so I can't order the sites correctly. Will raise a separate issue for this.
UMAP (for both datasets)
I've been running this analysis in R notebooks, using a dataframe generated by a python notebook. I cleaned this up and moved the relevant files to scratch_notebooks/figure_drafts/
For HK/19, the notebook generate_escape_dfs.ipynb, the resulting escape df, and the R notebook 230724_hk19_umap.Rmd are all in figure_drafts/umap_analysis/.
Corresponding files for Perth09 are all found under figure_drafts/perth09_analysis/
It would help streamline this if we can port the R analysis over to Python, let me know if you could also take a stab at that while you're testing the Perth09 PCA-UMAP @jbloom
jbloom
commented
1 year ago
Generate similar escape plots and UMAP analysis for data from previous Perth09 studies, plus some cleanup of current HK/19 DMS plots. Addresses the following points from @jbloom:
HongKong/2019
scratch_notebooks/figure_drafts/sitewise_escape/.Perth09
scratch_notebooks/figure_drafts/perth09_analysis.UMAP (for both datasets)
scratch_notebooks/figure_drafts/generate_escape_dfs.ipynb, the resulting escape df, and the R notebook230724_hk19_umap.Rmdare all infigure_drafts/umap_analysis/.figure_drafts/perth09_analysis/It would help streamline this if we can port the R analysis over to Python, let me know if you could also take a stab at that while you're testing the Perth09 PCA-UMAP @jbloom