domainogram | R Documentation |
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).
domainogram( Yi, x.s, x.e, w2y, xlim = NULL, wlim = NULL, colfun = makeColors, xlab = "", add = F, logskip = 1.01, ... )
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 |
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.
Benjamin Leblanc
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
calc.Qi, enrichmentScore, visualizationCoordinates, wSize2yAxis, makeColors, segmentation, plotOptimalSegments, plotDomains
# 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')
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