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# Track class for cytobands
# Author : Sylvain Mareschal <maressyl@gmail.com>
# License : GPL3 http://www.gnu.org/licenses/gpl.html
# Only defining new drawing parameters defaults
setRefClass(
Class = "track.bands",
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 <- 1000
params$label <- TRUE
params$labelStrand <- FALSE
params$labelCex <- 0.75
params$labelSrt <- 90
params$labelAdj <- "center"
params$labelOverflow <- FALSE
params$fillColor <- function() {
output <- slice$stain
output[ output == "gneg" ] <- "#EEEEEE"
output[ output == "gpos25" ] <- "#CCCCCC"
output[ output == "gpos50" ] <- "#AAAAAA"
output[ output == "gpos75" ] <- "#888888"
output[ output == "gpos100" ] <- "#666666"
output[ output == "acen" ] <- "#884444"
output[ output == "gvar" ] <- "#448844"
output[ output == "stalk" ] <- "#444488"
return(output)
}
params$border <- "#000000"
params$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.bands\" reference class object\n")
} else { cat("\n Extends \"track.bands\"\n")
}
# Inherited show()
callSuper(include=TRUE, fieldWidth=fieldWidth)
}
)
)
# Constructor
track.bands <- function(...) {
# Inheritance
object <- new("track.bands")
object$import(track.table(...))
return(object)
}
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