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FredHutch / gimap

This is under development R package for calculating genetic interactions
https://fredhutch.github.io/gimap/
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Add ability to select columns for the last sample replicates #39

Closed kweav closed 2 weeks ago

kweav commented 2 weeks ago

⚠️ This is a stacked PR based on PR #38 ⚠️ and should complete the described necessities/additions for 3 parameters as described in PR #35

This parameter for selecting columns doesn't directly impact a filter, but does impact two graphs. So there are only changes to the R/plots-qc.R file and the inst/rmd/gimapQCTemplate.Rmd file. Specifically impacting the qc_variance_hist() and qc_constructs_countzero_bar() functions. The changes to these functions include adding to the headers (param and description information), replacing anywhere numbers are hardcoded with the parameter, and sets the parameters to a default if they're null. Within the QC Template Rmd, changes include referencing the parameters in the function calls.

I can confirm that I knit the getting-started.Rmd successfully locally. The only oddity is that the heatmap is still showing up in the vignette rather than the QC report (as mentioned in PR #33)

Also need to setup something to check the identity of the target columns if they are not null as described in PR #38