nki-ccb/ppbc

Post-partum breast cancer

ppbc's Issues

Merge src/utils/outcome.R with src/spatial/process_density_outcomes.R

Handy to have just one function for processing outcome data, now that we have a "final" metadata file. outcome.R is the more robust of the two existing options and will also be used in the RNAseq pipeline post refactor. Both run and produce the desired result; low priority task.

Rerun analysis pipeline using "final" metadata

This is already WIP under the refactor branch. Incorporating a new metadata file requires a substantial rework of older notebooks. Where necessary, the code will be rewritten for legibility and polish as well as compatibility with the new file. Some reorganization is also taking place (i.e. RNAseq reports go in reports/rnaseq instead of reports).

Check the following enhancement when calculating density_total

Pertains to model_density.R.

# Also perform total aggregation on combined tumor and stroma
  totals <- region %>%    group_by(t_number, panel, cell_type, batch) %>%
    summarise(area = sum(area), n = sum(n), .groups = "drop") %>%
    mutate(classifier_label = "Total", .before = everything()) %>%
    group_by(classifier_label) %>%
    mutate(
      area = ensure_one_value(area), # Fill in area when n==0
      classifier_label = factor(classifier_label, levels = c("Stroma", "Tumor", "Total"))
    ) %>%
    mutate(density = if_else(n==0, 0, n / area))


  bind_rows(region, totals)
}

Unnecessarily copied code. How about

density_total <- density_per_region %>%
    group_by(t_number, panel, cell_type, batch, .drop=F) %>%
    summarize(n = sum(n), area = ensure_one_value(area)) %>%
    mutate(classifier_label = 'Total')

the density calculation from area and n can also be shared:

bind_rows(region, totals) %>%
    mutate(density = if_else(n==0, 0, n / area))

Originally posted by @tychobismeijer in #2 (comment)

Incorporate Hanne's code

All of Hanne's work is outside the git repo and based upon a mix of (mostly untracked) output files, sometimes with manual edits in Excel or similar. These need to be incorporated into version control before the project is reproducible.

Reworking the existing code to accept the "final" metadata file is a prerequisite, as her notebooks are based upon it.

Fix incidental lowercasing

Tumor is sometimes listed as "tumor" in the classifier label field. This should be fixed in the code that loads the data, not in model_density.R. It is not specific for density.

Originally posted by @tychobismeijer in #2 (comment)

Sample T20-62429 is excluded from spatial analysis

Find out why this sample is not working and fix or decide to exclude the sample permanently.

Move min_cell_count Snakemake parameters to config file.

rule invbf_time_density:
  input:
    density_outcome = "data/vectra/processed/density_ppbc.Rds",
    rmd="reports/spatial/06b_inv_time_density.Rmd",
    script="src/rmarkdown.R"
  params:
    min_cell_count = 20000,

Snakemake will not rerun if the parameters are changed. If they are in a seperate file, in input, it will rerun as expected.

Originally posted by @tychobismeijer in #2 (comment)

Refactor Cox regression notebook

Remove duplication and modularize regression functions for later reuse.

Set seed for secondary spatial stats?

It doesn't look like there's a seed set during the null model's random Poisson distribution. @tychobismeijer would you be opposed to setting a seed so that the results are 100% reproducible when the code is rerun?

R environment cannot be installed

Installation of renv fails for me, so this needs to be fixed or documented how installation is supposed to work.

Retrieving 'https://cloud.r-project.org/src/contrib/Archive/apeglm/apeglm_1.12.0.tar.gz' ...
Warning: failed to find source for 'bbmle 1.0.24' in package repositories
Warning: failed to find source for 'numDeriv 2020.2-1' in package repositories
Warning: failed to retrieve 'https://cloud.r-project.org/src/contrib/Archive/numDeriv/numDeriv_2020.2-1.tar.gz' [error code 22]
Warning: failed to retrieve 'https://cloud.r-project.org/src/contrib/Archive/apeglm/apeglm_1.12.0.tar.gz' [error code 22]
Error: failed to retrieve package '[email protected]'
In addition: Warning messages:
1: curl: (22) The requested URL returned error: 404  
2: failed to find source for 'bbmle 1.0.24' in package repositories 
3: curl: (22) The requested URL returned error: 404  
4: curl: (22) The requested URL returned error: 404  
Traceback (most recent calls last):
9: renv:::restore()
8: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
7: retrieve(packages)
6: handler(package, renv_retrieve_impl(package))
5: renv_retrieve_impl(package)
4: renv_retrieve_bioconductor(record)
3: renv_retrieve_repos(record)
2: stopf("failed to retrieve package '%s'", renv_record_format_remote(record))
1: stop(sprintf(fmt, ...), call. = call.)
Execution halted