Update pathway-analysis ORA notebook

[sjspielman]

We'll need to make these updates for Bioc 3.22:

1. We need to update this call and associated text as follows:

   • gs_cat -> gs_collection
   • gs_subcat -> gs_subcollection
   • CP:KEGG -> CP:KEGG_MEDICUS
     • Additional note here: This is the current version of KEGG. There is also CP:KEGG_LEGACY included, which matches the version we were last using and fully reproduces results. But, seems best to bump this. The resulting ORA gene sets are of course different but consistent and fine!
       

       training-modules/pathway-analysis/01-overrepresentation_analysis.Rmd

       Lines 131 to 133 in 6cea2a5

       	mm_kegg_df <- mm_msigdb_df |>
       	dplyr::filter(gs_cat == "C2", # curated gene sets
       	gs_subcat == "CP:KEGG") # KEGG pathways

       
       (and fix the tense typo while here):

       training-modules/pathway-analysis/01-overrepresentation_analysis.Rmd

       Line 136 in 6cea2a5

       *Note: We could specified that we wanted the KEGG gene sets using the `category` and `subcategory` arguments of `msigdbr()`, but we're going for general steps!*

2. Add some fig.width and/or fig.height to the plots, since we have more gene sets now and plots don't look great at the defaults.