Envest/calculate and plot delta kappa #72
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jaclyn-taroni
approved these changes
Oct 1, 2021
3-plot_category_kappa.R
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| left_join(null_array.list[[pair_index]], | ||
| by = c("perc.seq", "classifier", "norm.method")) %>% | ||
| mutate(delta_kappa = kappa.x - kappa.y) %>% # regular kappa - null kappa |
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I would use suffix here so that this can be a little more explicit:
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| left_join(null_array.list[[pair_index]], | |
| by = c("perc.seq", "classifier", "norm.method")) %>% | |
| mutate(delta_kappa = kappa.x - kappa.y) %>% # regular kappa - null kappa | |
| left_join(null_array.list[[pair_index]], | |
| by = c("perc.seq", "classifier", "norm.method"), | |
| suffix = c(".true", ".null")) %>% | |
| mutate(delta_kappa = kappa.true - kappa.null) %>% # regular kappa - null kappa |
If you make this change here, don't forget to apply it to the seq step below too!
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| # check that we have ordered pairs of regular and null files for array and seq | ||
| array_seeds <- stringr::str_sub(array.files, -8, -5) | ||
| null_array_seeds <- stringr::str_sub(null_array.files, -8, -5) | ||
| seq_seeds <- stringr::str_sub(seq.files, -8, -5) | ||
| null_seq_seeds <- stringr::str_sub(null_seq.files, -8, -5) |
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Hmmm... my instinct here is to suggest that we use other strings that we expect the seeds to be between to detect the seeds, but that seems potentially just as brittle to file name changes as the indexing.
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Agreed. Not sure what the best solution is. One mitigation of this is we have previously forced the seed to be a four digit number, so as long as it's the last thing to come before .tsv, it will be captured here.
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Brings #51 to a point where we can run all the scripts in full... fun weekend!
This PR modifies the existing
3-plot_category_kappa.Rto allow for delta kappas to be calculated, then uses the same plotting code. The--null_modeloption signals to the script to look for both the regular model and null model and take the difference in their kappa values (regular kappa minus null kappa). Throughout the script, a FALSE value fornull_modelresults in the same processing and output as before, and a TRUE value fornull_modeladds in additional steps viaif()statement blocks.:delta::kappa: Thanks!