R/filterTrack.R

In sheng-liu/sojourner: Statistical analysis of single molecule trajectories

## filterTrack-methods
##' @name filterTrack
##' @aliases filterTrack trimTrack trackLength
##' @title filterTrack
##' @rdname filterTrack-methods
##' @docType methods
##'
##' @description methods for filter and trim tracks based on track length.

##' @usage
##' filterTrack(trackll,filter=c(min=7,max=Inf))
##' trimTrack(trackll,trimmer=c(min=1,max=32))
##' trackLength(trackll)

##' @param trackll a list of track lists.
##' @param filter range of possible track lengths to keep
##' @param trimmer range of track lengths allowed in output, otherwise trimmed.


##' @return
##' \itemize{
##' \item{trackll} filtered or trimmed tracks.
##' \item{len} list of track lengths.
##' }

##' @details filterTrack() is used to filter out tracks that has length within 
##' a specified range (default 7~Inf). On the other hand, despite the lengths 
##' of tracks, trimTrack() is used to trim /cutoff all tracks to a specified 
##' range (default 1~32).
##'
##'
##' @examples
##' folder=system.file('extdata','SWR1',package='sojourner')
##' trackll=createTrackll(folder=folder, input=3)
##'
##' trackll.filter=filterTrack(trackll,filter=c(7,Inf))
##' trackll.trim=trimTrack(trackll,trimmer=c(1,20))
##'
##' # see the min and max length of the trackll
##' # trackLength() is a helper function output track length of trackll
##' lapply(trackLength(trackll),min)
##' lapply(trackLength(trackll.filter),min)
##'
##' lapply(trackLength(trackll),max)
##' lapply(trackLength(trackll.trim),max)
##'



##-----------------------------------------------------------------------------
## filterTrack

## a function to filter trackll based on specified fitler value
## (filterTrack on track length), default 6 frames/steps to Inf

##' @export filterTrack
filterTrack = function(trackll, filter = c(min = 7, max = Inf)) {
    
    # filter=match.arg(filter)
    
    # reinforce name
    names(filter) = c("min", "max")
    
    cat("applying filter, min", filter["min"], "  max", filter["max"], 
        "\n")
    
    track.len = list()
    for (i in seq_along(trackll)) {
        track.len[[i]] = vapply(trackll[[i]], function(track) {
            dim(track)[1]
        }, integer(1))
        trackll[[i]] = trackll[[i]][track.len[[i]] >= 
            filter["min"] & track.len[[i]] < filter["max"]]
    }
    
    return(trackll)
}


# no need for the focus swtich, as one can simply filter on a number
# that is bigger than the dt he wanted to draw on

##-----------------------------------------------------------------------------
## trim long tracks into shorter ones

.trimTrack = function(track, min = 1, max = 32) {
    t = track[min:max, ]
    cc.t = complete.cases(t)
    t = t[cc.t, ]
    return(t)
}

##' @export trimTrack
trimTrack = function(trackll, trimmer = c(min = 1, max = 32)) {
    
    # reinforce name
    names(trimmer) = c("min", "max")
    
    cat("applying trimmer, min", trimmer["min"], "  max", trimmer["max"], 
        "\n")
    
    
    trackll.trim = list()
    length(trackll.trim) = length(trackll)
    names(trackll.trim) = names(trackll)
    for (i in seq_along(trackll)) {
        trackll.trim[[i]] = lapply(trackll[[i]], 
            .trimTrack, min = trimmer["min"], max = trimmer["max"])
    }
    
    return(trackll.trim)
    
}

# max(sapply(x[[1]],dim))

##' @export trackLength
trackLength = function(trackll) {
    len = list()
    
    length(len) = length(trackll)
    names(len) = names(trackll)
    
    for (i in seq_along(trackll)) {
        len[[i]] = vapply(trackll[[i]], function(track) {
            dim(track)[1]
        }, integer(1))
    }
    return(len)
}