Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Question about percentile cutoffs in CellTagWhitelistFiltering function #22

Open
RoganGrant opened this issue Feb 13, 2023 · 0 comments

Comments

@RoganGrant
Copy link

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant