plotOccupancyProfile {ChIPanalyser} | R Documentation

## Plot Occupancy Profiles

### Description

`plotOccupancyProfile` plots the predicted profiles. If provided, this functions will also plot ChIP-seq profiles, PWMScores, DNAAccessibility, accuracy estimates and gene information.

### Usage

    plotOccupancyProfile(predictedProfile,setSequence,
        chipProfile = NULL,DNAAccessibility = NULL, occupancy = NULL,PWM=FALSE,
        occupancyProfileParameters = NULL,geneRef = NULL,axis=TRUE,...)

### Arguments

`predictedProfile` | `predictedProfile` is a `GRanges` containing predicted ChIP-seq scores for ONE loci and ONE combination of `lambda` ( See `ScalingFactorPWM` ) and `boundMolecules`.
`setSequence` | `setSequence` is a `GRanges` containing the locus of interest. This locus MUST be named.
`chipProfile` | `chipProfile` is a numeric vector containing real ChIP-seq scores.
`DNAAccessibility` | `DNAAccessibility` is a `GRanges` containing accesible DNA sites
`occupancy` | `occupancy` is a `GRanges` containing PWM Score and predicted Occupancies.
`PWM` | `PWM` is a logical value that in the case `occupancy` is provided which of occupancy scores of PWM scores hsould be plotted. Default set at FALSE
`occupancyProfileParameters` | `occupancyProfileParameters` is `occupancyProfileParameters` object containing parameters used for previous computations (see vignette for pipeline/function order)
`geneRef` | `geneRef` is a `GRanges` containing gene information on exons,introns, UTR's, enhancers or any other genetic element to be plotted.
`axis` | `axis` is a logical value indicating if axes should be plotted or not.
`...` | Any other graphical Parameter of the following : col, density, border, lty, lwd, cex, cex.axis, xlab, ylab, xlim, ylim, las and axislables. Each Parameter will be parsed in the same order as the arguments to this function. If the name of the argument is specified, the argument value will be parsed to the correct internal plotting. See examples below

### Details

Once the predicted ChIP-seq like profiles have been computed, it is possible to plot these profiles. The important aspect to keep in mind with `plotOccupancyProfile` is that in only computes one profile at a time. This means that the output of previous functions should be subsetted carefully. This leaves to the user more flexibility in what and how profiles should be plotted. Keep in mind that the output of different function are more or less nested.

### Value

Returns a porfile plot with "Occupancy" on the y axis and DNA position on the the X- axis. If the orange line is the predicted profile, the grey shaded area represents real ChIP-seq data. The yellow boxes represent regions on NON-accessible DNA. On the lower part of the plot, gene information is plotted with respect to the strand they are localised on. Finally, the blue vertical lines represent sites of either high Occupancy or high PWM score depending on which had been selected. The minimal plot will only contain the predicted profile. The more data is provided the more will be plotted.

### Author(s)

Patrick C.N. Martin <pm16057@essex.ac.uk>

### References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

### Examples

    #Data extraction
    data(ChIPanalyserData)
    # path to Position Frequency Matrix
    PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
    #As an example of genome, this example will run on the Drosophila genome

    if(!require("BSgenome.Dmelanogaster.UCSC.dm3", character.only = TRUE)){
        source("https://bioconductor.org/biocLite.R")
        biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
        }
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)
    #Building data objects
    GPP <- genomicProfileParameters(PFM=PFM,BPFrequency=DNASequenceSet)
    OPP <- occupancyProfileParameters()

    # Computing Genome Wide
    GenomeWide <- computeGenomeWidePWMScore(DNASequenceSet = DNASequenceSet,
        genomicProfileParameters = GPP)

    #Compute PWM Scores
    PWMScores <- computePWMScore(DNASequenceSet = DNASequenceSet,
        genomicProfileParameters = GenomeWide,
        setSequence = eveLocus, DNAAccessibility = Access)
    #Compute Occupnacy
    Occupancy <- computeOccupancy(AllSitesPWMScore = PWMScores,
        occupancyProfileParameters = OPP)

    #Compute ChIP profiles
    chipProfile <- computeChipProfile(setSequence = eveLocus,
        occupancy = Occupancy, occupancyProfileParameters = OPP)

    #Plotting Profile
    plotOccupancyProfile(predictedProfile=chipProfile[[1]][[1]],
        setSequence=eveLocus,
        chipProfile = eveLocusChip[[1]],
        DNAAccessibility = Access,
        occupancy = AllSitesAboveThreshold(Occupancy)[[1]][[1]],
        occupancyProfileParameters = OPP,
        geneRef =geneRef)

    ## Changing graphical Parameters

    #### In this examples ####
    ### predictedProfile will be reduce
    ### chipProfile will be blue
    ### and DNAAccessibility will be green
    plotOccupancyProfile(predictedProfile=chipProfile[[1]][[1]],
        setSequence=eveLocus,
        chipProfile = eveLocusChip[[1]],
        DNAAccessibility = Access,
        occupancy = AllSitesAboveThreshold(Occupancy)[[1]][[1]],
        occupancyProfileParameters = OPP,
        geneRef =geneRef,col=c("red","blue","green"))

    ### If name is specified
    plotOccupancyProfile(predictedProfile=chipProfile[[1]][[1]],
        setSequence=eveLocus,
        chipProfile = eveLocusChip[[1]],
        DNAAccessibility = Access,
        occupancy = AllSitesAboveThreshold(Occupancy)[[1]][[1]],
        occupancyProfileParameters = OPP,
        geneRef =geneRef,col=c("DNAAccessibility"="red","blue","green"))

[Package ChIPanalyser version 1.2.0 Index]