plotFootprints: Plots a footprint estimated by Centipede

In jianhong/ATACseqQC: ATAC-seq Quality Control

Plots a footprint estimated by Centipede

Description

Visualizing the footprint profile

Usage

plotFootprints(
  Profile,
  Mlen = 0,
  xlab = "Dist. to motif (bp)",
  ylab = "Cut-site probability",
  legLabels = c("For. strand", "Rev. strand"),
  legTitle,
  xlim,
  ylim,
  newpage = TRUE,
  motif,
  segmentation,
  reNormalizeByDistalSig = FALSE,
  ...
)

Arguments

Profile	A vector with the profile estimated by CENTIPEDE
Mlen	Length of the motif for drawing vertical lines delimiting it
xlab	Label of the x axis
ylab	Label for the y axis
legLabels	Labels for legend.
legTitle	Title for one of the plot corners
xlim	xlim
ylim	ylim
newpage	Plot the figure in a new page?
motif	a pfm object.
segmentation	the segmentation position and abundance
reNormalizeByDistalSig	Re-normalized the curver by distal signals.
...	Not used.

Value

Null.

Author(s)

Jianhong Ou

Examples

library(MotifDb)
CTCF <- query(MotifDb, c("CTCF"))
CTCF <- as.list(CTCF)
motif <- new("pfm", mat=CTCF[[1]], name="CTCF")
ATACseqQC:::plotFootprints(Profile=sample.int(500), 
                        Mlen=ncol(CTCF[[1]]), motif=motif)

jianhong/ATACseqQC documentation built on March 19, 2024, 8:30 a.m.