Scatterplot showing relative amounts of aberrant exon usage per sample

Description

Scatterplot showing sample-wise relative amounts (blue dots) of aberrant exon inclusion (horizontal axis) and exon skipping (vertical axis). Random sample-wise amounts calculated from permuted FIRMA scores can also be included in the plot (yellow dots).

Usage

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    scatterPlot(fileName, permutations, percentileHits, 
    permPercentileHits)

Arguments

fileName

Output filename. File format is optional, but must be one of png, jpg, eps or pdf.

permutations

Boolean argument to indicate whether permuted data should be included. 'TRUE' adds permutation data to the plot.

percentileHits

List with two items containing sample-wise numbers of exons denoted with aberrant exon skipping and inclusion, i.e., having FIRMA scores in the indicated lower and upper percentiles, respectively. This list is returned from the function 'aberrantExonUsage'.

permPercentileHits

List with two items containing random sample-wise numbers of exons denoted with aberrant exon skipping and inclusion, i.e., having FIRMA scores in the indicated lower and upper percentiles, respecively (calculated from FIRMA score permutations). This list is returned from the function 'probesetPermutations'.

Value

scatterPlot is used for the side-effect of producing a scatter plot showing relative amounts of aberrant exon usage per sample.

Examples

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    data(splicingFactors)
    fs <- firmaAnalysis(useToyData=TRUE)
    gs <- readGeneSummaries(useToyData=TRUE)
    tra <- aberrantExonUsage(1.0, fs)
#   The aberrantExonUsage function also creates the 'quantiles' object with
#   upper and lower threshold values for accepting aberrant exon usage, and
#   the list object 'aberrantExons' with the sample-wise number of exons
#   outside the threshold values.
    aberrantExonsPerms <- probesetPermutations(fs, quantiles)

# Create scatter plot with the samples
    scatterPlot("scatter.png", TRUE, aberrantExons, aberrantExonsPerms)