domainogram: Domainogram visualization

In benja0x40/MRA.TA: Multi Resolution Analysis of Tiling Arrays

Domainogram visualization

Description

Plot a domainogram from a sequence of log-transformed rank-based scores. This function allows to use a linear or log2 scale for window sizes (y axis).

Usage

domainogram(
  Yi,
  x.s,
  x.e,
  w2y,
  xlim = NULL,
  wlim = NULL,
  colfun = makeColors,
  xlab = "",
  add = F,
  logskip = 1.01,
  ...
)

Arguments

Yi	vector of statistical scores produced by the enrichmentScore function
x.s	vector of start coordinates (x axis) defining the represented genomic intervals.
x.e	vector of end coordinates (x axis) defining the represented genomic intervals.
w2y	coordinate mapping for window sizes (y axis) produced by the wSize2yAxis function.
xlim	range of the represented genomic region, which must be indicated as c(xmin, xmax).
wlim	range of represented window sizes, which must be indicated as c(wmin, wmax).
colfun	coloring function. The function makeColors is used by default.
xlab	legend of the x axis.
add	logical, when set to TRUE the plot should overlay an existing multi-resolution plot.
logskip	numeric coefficient for skipping the representation of window sizes when using the log2 scale on the y axis. A value of 1.0 forces to represent all window sizes. A value of 2 would double the window sizes represented at each iteration of the rendering.
...	optional parameters forwarded to the colfun function. When using the default makeColors function, these parameters are thresholds, colors, background and overflow (see documentation for details).

Details

The domainogram is a multi-resolution representation of scan statistics introduced by de Wit et al., 2008 (see references below). It is based on R.A. Fisher's method for the combination of p-values applied to non-parametric scores.

Author(s)

Benjamin Leblanc

References

de Wit E., Braunschweig U., Greil F., Bussemaker H.J., and van Steensel B. Global chromatin domain organization of the Drosophila genome. PLoS genetics 4: e1000045 (2008). http://dx.doi.org/10.1371/journal.pgen.1000045

See Also

calc.Qi, enrichmentScore, visualizationCoordinates, wSize2yAxis, makeColors, segmentation, plotOptimalSegments, plotDomains

Examples

# Simulate enrichment signal
n <- 500
Mi <- cos(2*pi*2.5*(-n:n)/n) + rnorm(2*n+1)
n <- length(Mi)

# Compute enrichment scores
Yi <- enrichmentScore(Mi)

# Visualization coordinates
x.s <- 1:n - 0.5
x.e <- 1:n + 0.5
w2y <- wSize2yAxis(n)

layout(matrix(1:2, 2, 1), heights=c(3,1)/4)
par(mar=c(3, 4, 1, 2)) # default bottom, left, top, right = c(5, 4, 4, 2)

# Plot domainogram
domainogram(Yi, x.s, x.e, w2y)
plot(Mi, type='l')

benja0x40/MRA.TA documentation built on March 13, 2023, 5:15 a.m.