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.
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
CellTagWhitelistFilteringstep, and noticed a discrepancy when I re-rendered the 90th percentile count cutoff. InCellTagWhitelistGeneration.R, the count cutoff is determined as follows: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.