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Question about percentile cutoffs in CellTagWhitelistFiltering function

Open RoganGrant opened this issue 2 years ago • 0 comments

First of all, thank you for this valuable package! We are beginning to use this tech in our lab quite frequently.

I wanted to re-plot the barcode rank / cutoff plot output during the CellTagWhitelistFiltering step, and noticed a discrepancy when I re-rendered the 90th percentile count cutoff. In CellTagWhitelistGeneration.R, the count cutoff is determined as follows:

count.cutoff <- quantile(count.sorted.table$Count, probs = percentile)
count.true.cut <- floor(count.cutoff/10)

I'm wondering what the rationale is behind dividing the count cutoff by 10? Likely there is something I'm missing.

On an unrelated note, is there any interest in switching to ggplot-based graphics? If so, I would be happy to submit a PR.

RoganGrant avatar Feb 13 '23 17:02 RoganGrant