plotOptimalSegments | R Documentation |
Plot optimal segments resulting from the segmentation function.
plotOptimalSegments( optimums, x.s, x.e, w2y, xlim = NULL, wlim = NULL, xlab = "", add = F, type = c("windows", "middles"), ... )
optimums |
data.frame of segmentation results generated by the segmentation 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). |
xlab |
legend of the x axis. |
add |
logical, when set to TRUE the plot should overlay an existing multi-resolution plot. |
type |
either "windows" (default) or "middles". |
... |
optional parameters forwarded to the |
Benjamin Leblanc
visualizationCoordinates, wSize2yAxis, domainogram, segmentation, plotDomains
# Simulate enrichment signal n <- 2000 Mi <- rep(0, n) Mi <- Mi + dnorm(1:n, 2.5*n/20, n/40) + dnorm(1:n, 4*n/20, 50) Mi <- Mi + 4 * dnorm(1:n, 5*n/10, n/10) Mi <- Mi + dnorm(1:n, 16*n/20, n/40) + dnorm(1:n, 17.5*n/20, 50) Mi <- (Mi/max(Mi))^4 + rnorm(n)/4 # Compute enrichment scores Yi <- enrichmentScore(Mi) # Multi-resolution segmentation seg.c <- segmentation(Yi, name="MRA_demo", wmin=20) # Load segmentation results opts <- read.delim(seg.c$file.segments, stringsAsFactors=F, skip=1) doms <- read.delim(seg.c$file.domains, stringsAsFactors=F) doms.mr <- read.delim(seg.c$file.maxresolution, stringsAsFactors=F) doms.ms <- read.delim(seg.c$file.maxscale, stringsAsFactors=F) # Visualization coordinates x.s <- 1:n - 0.5 x.e <- 1:n + 0.5 w2y <- wSize2yAxis(n, logscale=T) 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') # Visualize segmentation results plotOptimalSegments(opts, x.s, x.e, w2y, col="black") plot(Mi, type='l') # Visualize multi-resolution domains plotDomains(doms, x.s, x.e, w2y, col=rgb(0,0,0,0.5), border=rgb(0,0,0,0)) # Visualize max. resolution and max. scale domains plotDomains(doms.mr, x.s, x.e, w2y, col=rgb(0,1,0,0.5), border=rgb(0,0,0,0), lwd=2, lty=1, add=T) plotDomains(doms.ms, x.s, x.e, w2y, col=rgb(1,0,0,0.5), border=rgb(0,0,0,0), lwd=2, lty=1, add=T) legend("topright", c("Max. resolution", "Max. scale", "Both"), fill=c("green", "red", "chocolate"), bty='n') plot(Mi, type='l')
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