plotInterquantileWidth {CAGEr} | R Documentation

## Plot cluster widths

### Description

Histograms of the interquantile width of tag clusters or consensus clusters in each CAGE experiment.

### Usage

    plotInterquantileWidth(
      object,
      clusters = c("tagClusters", "consensusClusters"),
      tpmThreshold = 5,
      qLow = 0.1,
      qUp = 0.9,
      xlim = c(0, 150)
    )

    ## S4 method for signature 'CAGEexp'
    plotInterquantileWidth(
      object,
      clusters = c("tagClusters", "consensusClusters"),
      tpmThreshold = 5,
      qLow = 0.1,
      qUp = 0.9,
      xlim = c(0, 150)
    )

### Arguments

`object` | A `CAGEexp` object
`clusters` | `tagClusters` or `consensusClusters`.
`tpmThreshold` | Exclude clusters with normalized signal lower than `tpmThreshold`.
`qLow, qUp` | Quantile defining the 5' ("lower") and 3' ("upper") boundaries of the clusters.
`xlim` | Range of width to be plotted.

### Details

Interquantile width is a more robust measure of the promoter width than the total span of the region, because it takes into account the magnitude of the expression in the region. Positions of specified quantiles within each cluster have to be calculated beforehand by calling `quantilePositions`.

### Value

Plots the histograms with the `ggplot2` engine and returns the plot object invisibly.

### Author(s)

Vanja Haberle

Charles Plessy

### See Also

Other CAGEr plot functions: `hanabiPlot()`, `plotAnnot()`, `plotCorrelation()`, `plotExpressionProfiles()`, `plotReverseCumulatives()`

Other CAGEr clusters functions: `CTSSclusteringMethod()`, `CTSScumulativesTagClusters()`, `CustomConsensusClusters()`, `aggregateTagClusters()`, `clusterCTSS()`, `consensusClustersDESeq2()`, `consensusClustersGR()`, `cumulativeCTSSdistribution()`, `quantilePositions()`, `tagClustersGR()`

### Examples

    plotInterquantileWidth( exampleCAGEexp, clusters = "tagClusters"
                          , tpmThreshold = 50, qLow = 0.1, qUp = 0.9
                          , xlim = c(2,200))

    plotInterquantileWidth( exampleCAGEexp, clusters = "consensusClusters"
                          , tpmThreshold = 50, qLow = 0.1, qUp = 0.9
                          , xlim = c(2,200))

[Package CAGEr version 2.0.2 Index]