plot.genominator.coverage {Genominator} | R Documentation |
S3 method to plot genominator.coverage
object. Shows coverage as a function of plotting effort.
## S3 method for class 'genominator.coverage' plot(x, type = "l", col = NULL, draw.totals = TRUE, draw.legend = TRUE, legend.location = NULL, ...)
x |
An object of class |
type |
Plot type. See |
col |
Vector of plotting colors. |
draw.totals |
Logical indicating whether totals should be drawn. |
draw.legend |
Logical indicating whether legend should be drawn. |
legend.location |
Vector giving x and y coordinates of legend position. |
... |
Additional arguments for lower-level functions. |
This method is used for its side effect.
James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu
See Genominator
vignette for more information. See also computeCoverage
.
ed <- ExpData(system.file(package = "Genominator", "sample.db"), tablename = "raw") data("yeastAnno") a <- computeCoverage(ed, yeastAnno, effort = 2^(5:18), cutoff = function(x, ...) x > 1) plot(a, lwd = 5, col = "grey") plot(a, draw.totals = FALSE) ygroups <- rep(c("mut", "wt"), c(2,2)) b <- computeCoverage(ed, yeastAnno, grups = ygroups, effort = 2^(5:18), cutoff = function(x, ...) x > 1) plot(b) b <- computeCoverage(ed, yeastAnno, groups = ygroups, effort = 2^(5:18), cutoff = function(x, ...) x > 3, smooth = function(probs) { probs = probs + min(probs[probs!=0]) probs = probs/sum(probs) }) plot(b)