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# Track class for Copy Number Variations
# Author : Sylvain Mareschal <maressyl@gmail.com>
# License : GPL3 http://www.gnu.org/licenses/gpl.html
# Only defining new drawing parameters defaults
setRefClass(
Class = "track.CNV",
contains = "track.table",
methods = list(
defaultParams = function(...) {
"Returns class-specific defaults for graphical parameters. Inheriting class should overload it to define their own defaults.
- ... : may be used by inheriting methods, especially for inter-dependant parameters."
params <- callSuper(...)
params$drawFun <- "draw.boxes"
params$maxElements <- 2000
params$label <- FALSE
params$labelStrand <- FALSE
params$labelCex <- 0.75
params$labelSrt <- 0
params$labelAdj <- "left"
params$fillColor <- function() {
colors <- c(
"loss" = "#880000",
"loss mobile element" = "#880000",
"deletion" = "#FF8888",
"duplication" = "#8888FF",
"gain" = "#8888FF",
"tandem duplication" = "#8888FF",
"amplification" = "#000088",
"gain+loss" = "#BB7744",
"novel sequence insertion" = "#88FF88",
"mobile element insertion" = "#88FF88",
"insertion" = "#88FF88"
)
output <- colors[ as.character(slice$type) ]
output[ is.na(output) ] <- "#888888"
return(output)
}
params$border <- "fillColor"
params$height <- "3 cm"
params$xaxt <- "n"
params$yaxt <- "n"
params$ylim <- 0:1
params$cex.lab <- 1
return(params)
},
show = function(include=FALSE, fieldWidth=10) {
"Interactive printing
- include : single logical value, if TRUE class name will not be printed."
# Class name
if(!isTRUE(include)) { cat("\n \"track.CNV\" reference class object\n")
} else { cat("\n Extends \"track.CNV\"\n")
}
# Inherited show()
callSuper(include=TRUE, fieldWidth=fieldWidth)
}
)
)
# Constructor
track.CNV <- function(...) {
# Inheritance
object <- new("track.CNV")
object$import(track.table(...))
return(object)
}
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