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#' @name DataFrameQuantitativeTrack-class
#' @rdname DataFrameQuantitativeTrack-class
#' @exportClass DataFrameQuantitativeTrack
.DataFrameQuantitativeTrack <- setClass("DataFrameQuantitativeTrack",
contains="QuantitativeTrack",
slots=c(
coreObject="data.frame"
)
)
#----------------------------------------------------------------------------------------------------
#' Constructor for DataFrameQuantitativeTrack
#'
#' \code{DataFrameQuantitativeTrack} creates and \code{IGV} track for bed objects imported using \code{rtracklayer}
#'
#' Detailed description goes here
#'
#' @name DataFrameQuantitativeTrack
#' @rdname DataFrameQuantitativeTrack-class
#'
#' @param trackName A character string, used as track label by igv, we recommend unique names per track.
#' @param quantitativeData A base R \code{data.frame}
#' @param color A CSS color name (e.g., "red" or "#FF0000")
#' @param trackHeight track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
#' @param autoscale Autoscale track to maximum value in view
#' @param min Sets the minimum value for the data (y-axis) scale. Usually zero.
#' @param max Sets the maximum value for the data (y-axis) scale. This value is ignored if autoscale is TRUE
#' @param visibilityWindow Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types.
#'
#' @seealso DataFrameAnnotationTrack
#' @seealso GRangesQuantitativeTrack
#' @seealso GRangesAnnotationTrack
#' @seealso DataFrameAnnotationTrack
#' @seealso DataFrameQuantitativeTrack
#' @seealso GRangesAnnotationTrack
#' @seealso GRangesQuantitativeTrack
#' @seealso GenomicAlignmentTrack
#' @seealso UCSCBedAnnotationTrack
#' @seealso UCSCBedGraphQuantitativeTrack
#' @seealso VariantTrack
#' @seealso igvAnnotationTrack
#'
#' @return A DataFrameQuantitativeTrack object
#'
#' @examples
#' base.loc <- 88883100
#' tbl <- data.frame(chrom=rep("chr5", 3),
#' start=c(base.loc, base.loc+100, base.loc + 250),
#' end=c(base.loc + 50, base.loc+120, base.loc+290),
#' score=runif(3),
#' stringsAsFactors=FALSE)
#'
#' track <- DataFrameQuantitativeTrack("dataframeTest", tbl, autoscale=TRUE)
#'
#' @export
#'
DataFrameQuantitativeTrack <- function(trackName, quantitativeData, color="blue", trackHeight=50,
autoscale, min=NA_real_, max=NA_real_, visibilityWindow=100000)
{
stopifnot(ncol(quantitativeData) >= 4)
stopifnot(is.character(quantitativeData[, 1]))
stopifnot(is.numeric(quantitativeData[, 2]))
stopifnot(is.numeric(quantitativeData[, 3]))
stopifnot(is.numeric(quantitativeData[, 4]))
base.obj <- .QuantitativeTrack(Track(trackType="quantitative",
sourceType="file",
fileFormat="bedGraph",
trackName=trackName,
onScreenOrder=NA_integer_,
color=color,
height=trackHeight,
autoTrackHeight=FALSE,
minTrackHeight=50,
maxTrackHeight=500,
visibilityWindow=visibilityWindow),
autoscale=autoscale,
min=min,
max=max
)
stopifnot("data.frame" %in% is(quantitativeData))
obj <- .DataFrameQuantitativeTrack(base.obj, coreObject=quantitativeData)
} # DataFrameQuantitativeTrack
#----------------------------------------------------------------------------------------------------
#' Retrieve the size of the DataFrameQuantitativeTrack
#'
#' @param obj An object of class DataFrameQuantitativeTrack
#'
#' @return The number of elements
#'
#' @export
#'
setMethod("trackSize", "DataFrameQuantitativeTrack",
function(obj){
return(nrow(obj@coreObject))
})
#----------------------------------------------------------------------------------------------------
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