TSS Enrichment vs. Fragment Counts plot — plot_tss

Density scatter plot with log10(fragment_count) on the x-axis and TSS enrichment on the y-axis. This plot is most useful to select which cell barcodes in an experiment correspond to high-quality cells

Usage

plot_tss_scatter(
  atac_qc,
  min_frags = NULL,
  min_tss = NULL,
  bins = 100,
  apply_styling = TRUE
)

Arguments

atac_qc: Tibble as returned by qc_scATAC(). Must have columns nFrags and TSSEnrichment
min_frags: Minimum fragment count cutoff
min_tss: Minimum TSS Enrichment cutoff
bins: Number of bins for density calculation
apply_styling: If false, return a plot without pretty styling applied

Examples

## Prep data
frags <- get_demo_frags(filter_qc = FALSE, subset = FALSE)
genes <- read_gencode_transcripts(
  file.path(tempdir(), "references"), release = "42",
  annotation_set = "basic",
  features = "transcript"
)
blacklist <- read_encode_blacklist(file.path(tempdir(), "references"), genome="hg38")
atac_qc <- qc_scATAC(frags, genes, blacklist)


## Render tss enrichment vs fragment plot
plot_tss_scatter(atac_qc, min_frags = 1000, min_tss = 10)