plot_ABC: plot compartments from samples A & B, perhaps by diffing...

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

FIXME: use an exponential smoother instead of the mean smoother

Usage

plot_ABC(
  A,
  B,
  diff = TRUE,
  with = TRUE,
  what = "counts",
  steps = 1L,
  nameA = "A",
  nameB = "B",
  ...
)

Arguments

A	a GRanges, usually from compartmap or get_AB
B	a GRanges, usually from compartmap or get_AB (but see Details)
diff	plot their differences, too? (TRUE, and again, see Details)
with	plot with confidence intervals? (TRUE; yet again, see Details)
what	what assay fed the original A and B calls? (also, see Details)
steps	damping step if using mean smoother – default is 1, no smooth
nameA	name for A in the plots ("A")
nameB	name for B in the plots ("B")
...	more parameters to feed to diff_AB
mat	difference correlation matrices instead? (FALSE, experimental)

Details

There are two nonstandard options here, neither of which should be used just yet (if it breaks, you get to keep the pieces, but I'm happy to accept PRs). The first is if what is set to "ratio" – the assumption is that we are looking at "chromatin potential" and, accordingly, the function will assume that A, B, or both were generated from both spliced and unspliced counts. The second is if both diff and with are specified; then the CIs will be treated as upper and lower bounds for the differences in a third panel. The behavior of this function is undefined if diff and with are TRUE along with what being set to "ratio". The behavior of this function is also undefined if mat is set to true, not because it's particularly hard, but because the difference detection is a work in progress.

See Also

  compartmap::plotAB

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.