plotDifferential: Plot differential contacts

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Plot differential contacts

Description

Plot differential contacts

Usage

plotDifferential(umi4c, grouping = NULL, colors = NULL, xlim = NULL)

Arguments

umi4c	UMI4C object as generated by makeUMI4C.
grouping	Grouping used for the different samples. If none available or want to add new groupings, run addGrouping.
colors	Named vector of colors to use for plotting for each group.
xlim	Limits for the plot x axis (genomic coordinates).

Value

Produces a plot of the fold changes at the differential regions analyzed ghat are contained in the UMI4C object.

Examples

data("ex_ciita_umi4c")
ex_ciita_umi4c <- addGrouping(ex_ciita_umi4c, grouping="condition")

enh <- GRanges(c("chr16:10925006-10928900", "chr16:11102721-11103700"))
umi_dif <- fisherUMI4C(ex_ciita_umi4c, query_regions = enh, 
                       filter_low = 20, resize = 5e3)
plotDifferential(umi_dif)

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.