R/AllClasses.R
In RGLab/Pviz: Peptide Annotation and Data Visualization using Gviz
Defines functions
DTrack
ATrack
ProbeTrack
ProteinSequenceTrack
ProteinAxisTrack
Documented in
ATrack
DTrack
ProbeTrack
ProteinAxisTrack
ProteinSequenceTrack
#' DTrack class
#'
#' This class contains Gviz's DataTrack and adds default values to the genome and
#' chromosome slot
#'
#' Refer to \code{DataTrack} for details regarding the constructor.
#'
#' @seealso \code{\link{DataTrack}}, \code{\link{GdObject}}
#'
#' @examples
#' dTrack <- DTrack(start=seq(1,1000, len=100), width=10, data=matrix(runif(400),
#' nrow=4), name="random data")
#'
#' @name DTrack
#' @aliases DTrack-class
## @importClassesFrom Gviz DataTrack NumericTrack RangeTrack GdObject
#' @author Renan Sauteraud
#' @export
setClass("DTrack", contains = "DataTrack", representation = representation())
setMethod("initialize", "DTrack", function(.Object, ...){
.Object <- callNextMethod() #Call the initialize function of Gviz::DataTrack
return(.Object)
})
#' @rdname DTrack
#' @param range,start,end,width,data,name,... Arguments to be passed to
#' \code{DataTrack}.
#' @export
DTrack <- function(range=NULL, start=NULL, end=NULL, width=NULL, data,
name="DTrack", ...){
GvizDataTrack<-DataTrack(range=range, start=start, end=end, width=width,
name=name, chromosome="chr0", strand="*", genome="all",
data=data, ...)
#Create DTrack object using the slots of the DataTrack
new("DTrack", range=GvizDataTrack@range,
data=GvizDataTrack@data,
chromosome=GvizDataTrack@chromosome,
genome=GvizDataTrack@genome,
strand=GvizDataTrack@strand,
name=GvizDataTrack@name,
...)
}
#' ATrack class
#'
#' This class contains Gviz's AnnotationTrack and adds default values to the genome and
#' chromosome slot
#'
#' @seealso \code{\link{AnnotationTrack}}, \code{\link{GdObject}}
#'
#' @examples
#' # Object construction
#' aTrack <- ATrack(start = c(20, 60), end = c(40, 100), name = "random.anno",
#' id=c("small","big"))
#' #Stacking example
#' a2Track <- ATrack(start = c(20, 30), end = c(40, 100), name = "stacking=dense",
#' id = c("small", "big"), stacking = "dense", fill=c("black", "orange"))
#' a3Track <- ATrack(start = c(20, 30), end = c(40, 100), name = "no stacking",
#' id = c("small", "big"), fill = c("black", "orange"))
#' #Plotting
#' plotTracks(trackList = c(aTrack, a2Track, a3Track), showFeatureId = TRUE)
#'
#' @name ATrack
#' @aliases ATrack-class
## @importClassesFrom Gviz AnnotationTrack StackedTrack RangeTrack GdObject
#' @author Renan Sauteraud
#' @export
setClass("ATrack", contains="AnnotationTrack", representation=representation())
setMethod("initialize", "ATrack", function(.Object, ...){
.Object <- callNextMethod() #Call the initialize function of Gviz::AnnotationTrack
return(.Object)
})
#' @rdname ATrack
#' @param range,start,end,width,group,id,stacking,name,fun,selectFun,...
#' Arguments to be passed to \code{AnnotationTrack}.
#' @export
ATrack <- function(range=NULL, start=NULL, end=NULL, width=NULL, group,
id, stacking="squish", name="ATrack", fun, selectFun, ...){
#Create an AnnotationTrack object
GvizAnnotationTrack<-AnnotationTrack(range=range, start=start, end=end, width=width,
id=id, name=name, chromosome="chr0", genome="all", stacking=stacking,
fun=fun, selectFun=selectFun, ...)
#Create ATrack using the AnnotationTrack
new("ATrack", range=GvizAnnotationTrack@range,
chromosome=GvizAnnotationTrack@chromosome,
genome=GvizAnnotationTrack@genome,
name=GvizAnnotationTrack@name,
stacking=GvizAnnotationTrack@stacking,
...)
}
#' ProbeTrack
#'
#' This track can be used to display the frequency of antibody binding for each
#' probe on an arrayas predicted by \code{pepStat}'s function \code{makeCalls}.
#'
#' @slot sequence A \code{character} vector. The probes sequence.
#' @slot probeStart A \code{numeric} vector. The start position of the probes.
#' @slot intensity A \code{numeric} vector. The frequency of response of each probe.
#' Or the baseline corrected intensity of the signal.
#'
#' @seealso \code{\link{GdObject}}
#'
#' @inheritParams DTrack
#'
#' @examples
#' if(require(pepDat)){
#' data(restab)
#' pt <- ProbeTrack(sequence = restab$peptide,
#' intensity = restab$group2,
#' probeStart = restab$start)
#' plotTracks(pt)
#' plotTracks(pt, from = 460, to = 560, legend=TRUE)
#' }
#'
#' @name ProbeTrack
#' @aliases ProbeTrack-class
#' @author Renan Sauteraud
## @importClassesFrom Gviz GdObject
#' @export
setClass("ProbeTrack", contains = "GdObject",
representation(sequence="list", intensity = "list", probeStart = "list"),
prototype(
sequence=list(),
intensity = list(),
probeStart = list(),
dp = DisplayPars(
color=rev(heat.colors(8, alpha = 1)),
size = 2, #it displays better when slightly bigger than annotation tracks
cex=1
)
)
)
setMethod("initialize", "ProbeTrack", function(.Object, sequence, intensity, probeStart, name, ...){
.makeParMapping()
.Object@name <- name
.Object@sequence <- sequence
.Object@intensity <- intensity
.Object@probeStart <- probeStart
.Object <- callNextMethod(.Object, ...) #Call the initialize function of Gviz::GdObject
return(.Object)
})
#' @rdname ProbeTrack
#' @param sequence A \code{character} vector. The sequence of peptides to
#' display.
#' @param intensity A \code{numeric} vector. The frequency of binding or the
#' baseline corrected intensity for the peptides.
#' @param probeStart A \code{numeric} vector. The start position of the peptides.
#' @param name A \code{character}. The name of the track used in the title panel
#' when plotting
#' @param restab A \code{data.frame} containing all the above parameters, as
#' outputted by \code{pepStat}'s \code{restab} function.
#' @param group A \code{character}. The group to display on the \code{ProbeTrak}.
#' This is only required when \code{restab} is not NULL. See details section
#' for more information.
#'
#' @details
#' The vectors for the arguments \code{sequence}, \code{freq} and
#' \code{probeStart} should be of the same length. If \code{restab} is provided,
#' the three previous arguments will be ignored and \code{group} must be
#' specified. \code{group} must be a valid column name in \code{restab},
#' \code{data.frame}.
#'
#' @seealso \code{restab}
#'
#' @export
ProbeTrack <- function(sequence, intensity, probeStart, restab = NULL,
group = NULL, name="ProbeTrack", ...){
if(!is.null(restab) && class(restab) == "data.frame"){
if(is.null(group) || !(group %in% colnames(restab))){
stop("'group' has to be a valid column name in 'restab'")
}
sequence <- list(restab$names)
probeStart <- list(restab$start)
intensity <- list(restab[, group])
} else{
if(missing(probeStart)){
stop("Need probeStart argument to know where to plot the data on the genome")
}
if(missing(sequence)){
stop("Need sequence argument to know what to plot")
}
if(class(sequence)!="list"){
sequence<-list(sequence)
intensity<-list(intensity)
probeStart<-list(probeStart)
}
}
##check the consistancy of number of entires
if(!(identical(lapply(intensity,length),lapply(probeStart,length)) && identical(lapply(sequence,length),lapply(probeStart,length))))
stop("sequence, intensity and probeStart need have identifcal structure!")
##check the types
if(any(unlist(lapply(sequence,class))!="character"))
stop("sequence has to be character vector!")
if(any(unlist(lapply(intensity,class))!="numeric")||any(!unlist(lapply(probeStart,class))%in%c("numeric","integer")))
stop("intensity and probeStart have to be numeric vectors!")
new("ProbeTrack", sequence=sequence, intensity=intensity, probeStart=probeStart, name=name, ...)
}
#' ProteinSequenceTrack
#'
#' A track to display peptides and protein sequences.
#'
#' @seealso \code{\link{SequenceTrack}}, \code{\link{DisplayPars}}
#'
#' @author Renan Sauteraud
#'
#' @name ProteinSequenceTrack
#' @aliases ProteinSequenceTrack-class
#' @importFrom GenomicRanges GRanges
#' @importFrom IRanges IRanges
#' @importFrom IRanges IRanges
#' @importFrom biovizBase getBioColor
#' @importFrom Biostrings AA_ALPHABET
## @importClassesFrom Gviz GdObject
#' @export
#'
setClass("ProteinSequenceTrack",
contains = "GdObject",
representation = representation(sequence = "character",
chromosome = "character", genome = "character"),
prototype = prototype(name = "Sequence", chromosome = "chr0", genome = "all")
)
#' @rdname ProteinSequenceTrack
#' @param sequence A \code{character} or \code{AAString} of length one. The
#' sequence to display.
#' @param name A \code{character}. The name of the track used in the title panel
#' when plotting
#' @param ... Additional items which will all be interpreted as display
#' parameters.
#'
#' @examples
#' if(require(pepDat)){
#' data(pep_hxb2)
#' hxb2_seq <- metadata(pep_hxb2)$sequence
#' st<-ProteinSequenceTrack(sequence=hxb2_seq, name="env")
#'
#' # Plotting amino acids
#' plotTracks(st, to = 20)
#'
#' # When the range becomes wider, only coloured squares are displayed
#' plotTracks(st, to = 100)
#'
#' # When overplotting, a single line will mark the ProteinSequenceTrack
#' plotTracks(st)
#' }
#'
#' @export
ProteinSequenceTrack <- function(sequence=NULL, name = "Sequence", ...){
if(is.null(sequence)){
stop("A 'character' or 'AAString' object should be supplied")
}
sequence<-as.character(sequence)
pst <- new("ProteinSequenceTrack", chromosome = "chr0", genome = "all", name = name, ...)
displayPars(pst)$fontcolor <- getBioColor(type="AA_ALPHABET")
displayPars(pst)$size <- 0.25
pst@sequence <- sequence
return(pst)
}
#' ProteinAxisTrack
#'
#' A track to display an axis for protein or peptide sequences
#'
#' @seealso \code{\link{GenomeAxisTrack}}
#'
#' @author Renan Sauteraud
#'
#' @name ProteinAxisTrack
#' @aliases ProteinAxisTrack-class
#' @export
#'
setClass("ProteinAxisTrack",
contains = "GenomeAxisTrack",
representation(addNC = "logical"),
prototype(addNC = FALSE, dp = DisplayPars(lwd = 2))
)
setMethod("initialize", "ProteinAxisTrack", function(.Object, addNC, name, ...){
.makeParMapping()
.Object@addNC<-addNC
.Object@name<-name
.Object<-callNextMethod(.Object, ...)
})
#' @rdname ProteinAxisTrack
#' @param range,name,id,... Arguments to be passed to \code{GenomeAxisTrack}.
#' @param addNC A \code{logical}. If TRUE, display the Amino-terminal and
#' Carboxyl-terminal ends on the axis.
#'
#' @examples
#' # Object construction
#' paxTrack <- ProteinAxisTrack()
#' pax2 <- ProteinAxisTrack(addNC=TRUE)
#' pax3 <- ProteinAxisTrack(littleTicks=TRUE)
#' # Plotting
#' plotTracks(c(paxTrack,pax2,pax3), from=1, to=100)
#'
#' @export
ProteinAxisTrack<-function(range=NULL, name="Axis", addNC=FALSE, id=NULL, ...){
GvizGAT<-new("GenomeAxisTrack", name=name, range=range, id=id, ...)
new("ProteinAxisTrack",range=GvizGAT@range,
name=GvizGAT@name,
id=GvizGAT@id,
addNC=addNC, ...)
}
RGLab/Pviz documentation built on Nov. 6, 2019, 5 p.m.
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Defines functions DTrack ATrack ProbeTrack ProteinSequenceTrack ProteinAxisTrack
Documented in ATrack DTrack ProbeTrack ProteinAxisTrack ProteinSequenceTrack
#' DTrack class
#'
#' This class contains Gviz's DataTrack and adds default values to the genome and
#' chromosome slot
#'
#' Refer to \code{DataTrack} for details regarding the constructor.
#'
#' @seealso \code{\link{DataTrack}}, \code{\link{GdObject}}
#'
#' @examples
#' dTrack <- DTrack(start=seq(1,1000, len=100), width=10, data=matrix(runif(400),
#' nrow=4), name="random data")
#'
#' @name DTrack
#' @aliases DTrack-class
## @importClassesFrom Gviz DataTrack NumericTrack RangeTrack GdObject
#' @author Renan Sauteraud
#' @export
setClass("DTrack", contains = "DataTrack", representation = representation())
setMethod("initialize", "DTrack", function(.Object, ...){
.Object <- callNextMethod() #Call the initialize function of Gviz::DataTrack
return(.Object)
})
#' @rdname DTrack
#' @param range,start,end,width,data,name,... Arguments to be passed to
#' \code{DataTrack}.
#' @export
DTrack <- function(range=NULL, start=NULL, end=NULL, width=NULL, data,
name="DTrack", ...){
GvizDataTrack<-DataTrack(range=range, start=start, end=end, width=width,
name=name, chromosome="chr0", strand="*", genome="all",
data=data, ...)
#Create DTrack object using the slots of the DataTrack
new("DTrack", range=GvizDataTrack@range,
data=GvizDataTrack@data,
chromosome=GvizDataTrack@chromosome,
genome=GvizDataTrack@genome,
strand=GvizDataTrack@strand,
name=GvizDataTrack@name,
...)
}
#' ATrack class
#'
#' This class contains Gviz's AnnotationTrack and adds default values to the genome and
#' chromosome slot
#'
#' @seealso \code{\link{AnnotationTrack}}, \code{\link{GdObject}}
#'
#' @examples
#' # Object construction
#' aTrack <- ATrack(start = c(20, 60), end = c(40, 100), name = "random.anno",
#' id=c("small","big"))
#' #Stacking example
#' a2Track <- ATrack(start = c(20, 30), end = c(40, 100), name = "stacking=dense",
#' id = c("small", "big"), stacking = "dense", fill=c("black", "orange"))
#' a3Track <- ATrack(start = c(20, 30), end = c(40, 100), name = "no stacking",
#' id = c("small", "big"), fill = c("black", "orange"))
#' #Plotting
#' plotTracks(trackList = c(aTrack, a2Track, a3Track), showFeatureId = TRUE)
#'
#' @name ATrack
#' @aliases ATrack-class
## @importClassesFrom Gviz AnnotationTrack StackedTrack RangeTrack GdObject
#' @author Renan Sauteraud
#' @export
setClass("ATrack", contains="AnnotationTrack", representation=representation())
setMethod("initialize", "ATrack", function(.Object, ...){
.Object <- callNextMethod() #Call the initialize function of Gviz::AnnotationTrack
return(.Object)
})
#' @rdname ATrack
#' @param range,start,end,width,group,id,stacking,name,fun,selectFun,...
#' Arguments to be passed to \code{AnnotationTrack}.
#' @export
ATrack <- function(range=NULL, start=NULL, end=NULL, width=NULL, group,
id, stacking="squish", name="ATrack", fun, selectFun, ...){
#Create an AnnotationTrack object
GvizAnnotationTrack<-AnnotationTrack(range=range, start=start, end=end, width=width,
id=id, name=name, chromosome="chr0", genome="all", stacking=stacking,
fun=fun, selectFun=selectFun, ...)
#Create ATrack using the AnnotationTrack
new("ATrack", range=GvizAnnotationTrack@range,
chromosome=GvizAnnotationTrack@chromosome,
genome=GvizAnnotationTrack@genome,
name=GvizAnnotationTrack@name,
stacking=GvizAnnotationTrack@stacking,
...)
}
#' ProbeTrack
#'
#' This track can be used to display the frequency of antibody binding for each
#' probe on an arrayas predicted by \code{pepStat}'s function \code{makeCalls}.
#'
#' @slot sequence A \code{character} vector. The probes sequence.
#' @slot probeStart A \code{numeric} vector. The start position of the probes.
#' @slot intensity A \code{numeric} vector. The frequency of response of each probe.
#' Or the baseline corrected intensity of the signal.
#'
#' @seealso \code{\link{GdObject}}
#'
#' @inheritParams DTrack
#'
#' @examples
#' if(require(pepDat)){
#' data(restab)
#' pt <- ProbeTrack(sequence = restab$peptide,
#' intensity = restab$group2,
#' probeStart = restab$start)
#' plotTracks(pt)
#' plotTracks(pt, from = 460, to = 560, legend=TRUE)
#' }
#'
#' @name ProbeTrack
#' @aliases ProbeTrack-class
#' @author Renan Sauteraud
## @importClassesFrom Gviz GdObject
#' @export
setClass("ProbeTrack", contains = "GdObject",
representation(sequence="list", intensity = "list", probeStart = "list"),
prototype(
sequence=list(),
intensity = list(),
probeStart = list(),
dp = DisplayPars(
color=rev(heat.colors(8, alpha = 1)),
size = 2, #it displays better when slightly bigger than annotation tracks
cex=1
)
)
)
setMethod("initialize", "ProbeTrack", function(.Object, sequence, intensity, probeStart, name, ...){
.makeParMapping()
.Object@name <- name
.Object@sequence <- sequence
.Object@intensity <- intensity
.Object@probeStart <- probeStart
.Object <- callNextMethod(.Object, ...) #Call the initialize function of Gviz::GdObject
return(.Object)
})
#' @rdname ProbeTrack
#' @param sequence A \code{character} vector. The sequence of peptides to
#' display.
#' @param intensity A \code{numeric} vector. The frequency of binding or the
#' baseline corrected intensity for the peptides.
#' @param probeStart A \code{numeric} vector. The start position of the peptides.
#' @param name A \code{character}. The name of the track used in the title panel
#' when plotting
#' @param restab A \code{data.frame} containing all the above parameters, as
#' outputted by \code{pepStat}'s \code{restab} function.
#' @param group A \code{character}. The group to display on the \code{ProbeTrak}.
#' This is only required when \code{restab} is not NULL. See details section
#' for more information.
#'
#' @details
#' The vectors for the arguments \code{sequence}, \code{freq} and
#' \code{probeStart} should be of the same length. If \code{restab} is provided,
#' the three previous arguments will be ignored and \code{group} must be
#' specified. \code{group} must be a valid column name in \code{restab},
#' \code{data.frame}.
#'
#' @seealso \code{restab}
#'
#' @export
ProbeTrack <- function(sequence, intensity, probeStart, restab = NULL,
group = NULL, name="ProbeTrack", ...){
if(!is.null(restab) && class(restab) == "data.frame"){
if(is.null(group) || !(group %in% colnames(restab))){
stop("'group' has to be a valid column name in 'restab'")
}
sequence <- list(restab$names)
probeStart <- list(restab$start)
intensity <- list(restab[, group])
} else{
if(missing(probeStart)){
stop("Need probeStart argument to know where to plot the data on the genome")
}
if(missing(sequence)){
stop("Need sequence argument to know what to plot")
}
if(class(sequence)!="list"){
sequence<-list(sequence)
intensity<-list(intensity)
probeStart<-list(probeStart)
}
}
##check the consistancy of number of entires
if(!(identical(lapply(intensity,length),lapply(probeStart,length)) && identical(lapply(sequence,length),lapply(probeStart,length))))
stop("sequence, intensity and probeStart need have identifcal structure!")
##check the types
if(any(unlist(lapply(sequence,class))!="character"))
stop("sequence has to be character vector!")
if(any(unlist(lapply(intensity,class))!="numeric")||any(!unlist(lapply(probeStart,class))%in%c("numeric","integer")))
stop("intensity and probeStart have to be numeric vectors!")
new("ProbeTrack", sequence=sequence, intensity=intensity, probeStart=probeStart, name=name, ...)
}
#' ProteinSequenceTrack
#'
#' A track to display peptides and protein sequences.
#'
#' @seealso \code{\link{SequenceTrack}}, \code{\link{DisplayPars}}
#'
#' @author Renan Sauteraud
#'
#' @name ProteinSequenceTrack
#' @aliases ProteinSequenceTrack-class
#' @importFrom GenomicRanges GRanges
#' @importFrom IRanges IRanges
#' @importFrom IRanges IRanges
#' @importFrom biovizBase getBioColor
#' @importFrom Biostrings AA_ALPHABET
## @importClassesFrom Gviz GdObject
#' @export
#'
setClass("ProteinSequenceTrack",
contains = "GdObject",
representation = representation(sequence = "character",
chromosome = "character", genome = "character"),
prototype = prototype(name = "Sequence", chromosome = "chr0", genome = "all")
)
#' @rdname ProteinSequenceTrack
#' @param sequence A \code{character} or \code{AAString} of length one. The
#' sequence to display.
#' @param name A \code{character}. The name of the track used in the title panel
#' when plotting
#' @param ... Additional items which will all be interpreted as display
#' parameters.
#'
#' @examples
#' if(require(pepDat)){
#' data(pep_hxb2)
#' hxb2_seq <- metadata(pep_hxb2)$sequence
#' st<-ProteinSequenceTrack(sequence=hxb2_seq, name="env")
#'
#' # Plotting amino acids
#' plotTracks(st, to = 20)
#'
#' # When the range becomes wider, only coloured squares are displayed
#' plotTracks(st, to = 100)
#'
#' # When overplotting, a single line will mark the ProteinSequenceTrack
#' plotTracks(st)
#' }
#'
#' @export
ProteinSequenceTrack <- function(sequence=NULL, name = "Sequence", ...){
if(is.null(sequence)){
stop("A 'character' or 'AAString' object should be supplied")
}
sequence<-as.character(sequence)
pst <- new("ProteinSequenceTrack", chromosome = "chr0", genome = "all", name = name, ...)
displayPars(pst)$fontcolor <- getBioColor(type="AA_ALPHABET")
displayPars(pst)$size <- 0.25
pst@sequence <- sequence
return(pst)
}
#' ProteinAxisTrack
#'
#' A track to display an axis for protein or peptide sequences
#'
#' @seealso \code{\link{GenomeAxisTrack}}
#'
#' @author Renan Sauteraud
#'
#' @name ProteinAxisTrack
#' @aliases ProteinAxisTrack-class
#' @export
#'
setClass("ProteinAxisTrack",
contains = "GenomeAxisTrack",
representation(addNC = "logical"),
prototype(addNC = FALSE, dp = DisplayPars(lwd = 2))
)
setMethod("initialize", "ProteinAxisTrack", function(.Object, addNC, name, ...){
.makeParMapping()
.Object@addNC<-addNC
.Object@name<-name
.Object<-callNextMethod(.Object, ...)
})
#' @rdname ProteinAxisTrack
#' @param range,name,id,... Arguments to be passed to \code{GenomeAxisTrack}.
#' @param addNC A \code{logical}. If TRUE, display the Amino-terminal and
#' Carboxyl-terminal ends on the axis.
#'
#' @examples
#' # Object construction
#' paxTrack <- ProteinAxisTrack()
#' pax2 <- ProteinAxisTrack(addNC=TRUE)
#' pax3 <- ProteinAxisTrack(littleTicks=TRUE)
#' # Plotting
#' plotTracks(c(paxTrack,pax2,pax3), from=1, to=100)
#'
#' @export
ProteinAxisTrack<-function(range=NULL, name="Axis", addNC=FALSE, id=NULL, ...){
GvizGAT<-new("GenomeAxisTrack", name=name, range=range, id=id, ...)
new("ProteinAxisTrack",range=GvizGAT@range,
name=GvizGAT@name,
id=GvizGAT@id,
addNC=addNC, ...)
}
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