plotAggregateCoverage {periodicDNA} | R Documentation

## A function to plot aggregated signals over sets of GRanges

### Description

This function takes one or several RleList genomic tracks (e.g. imported by rtraklayer::import(..., as = 'Rle')) and one or several GRanges objects. It computes coverage of the GRanges by the genomic tracks and returns an aggregate coverage plot.

### Usage

    plotAggregateCoverage(x, ...)

    ## S3 method for class 'CompressedRleList'
    plotAggregateCoverage(x, granges, ...)

    ## S3 method for class 'SimpleRleList'
    plotAggregateCoverage(
      x,
      granges,
      colors = NULL,
      xlab = "Center of elements",
      ylab = "Score",
      xlim = NULL,
      ylim = NULL,
      quartiles = c(0.025, 0.975),
      verbose = FALSE,
      bin = 1,
      plot_central = TRUE,
      run_in_parallel = FALSE,
      split_by_granges = FALSE,
      norm = "none",
      ...
    )

    ## S3 method for class 'list'
    plotAggregateCoverage(
      x,
      granges,
      colors = NULL,
      xlab = "Center of elements",
      ylab = "Score",
      xlim = NULL,
      ylim = NULL,
      quartiles = c(0.025, 0.975),
      verbose = FALSE,
      bin = 1,
      plot_central = TRUE,
      split_by_granges = TRUE,
      split_by_track = FALSE,
      free_scales = FALSE,
      run_in_parallel = FALSE,
      norm = "none",
      ...
    )

### Arguments

`x` | a single signal track (CompressedRleList or SimpleRleList class), or several signal tracks (SimpleRleList or CompressedRleList class) grouped in a named list
`...` | additional parameters
`granges` | a GRanges object or a named list of GRanges
`colors` | a vector of colors
`xlab` | x axis label
`ylab` | y axis label
`xlim` | y axis limits
`ylim` | y axis limits
`quartiles` | Which quantiles to use to determine y scale automatically?
`verbose` | Boolean
`bin` | Integer Width of the window to use to smooth values by zoo::rollMean
`plot_central` | Boolean Draw a vertical line at 0
`run_in_parallel` | Boolean Should the plots be computed in parallel using mclapply?
`split_by_granges` | Boolean Facet plots over the sets of GRanges
`norm` | character Should the signal be normalized ('none', 'zscore' or 'log2')?
`split_by_track` | Boolean Facet plots by the sets of signal tracks
`free_scales` | Boolean Should each facet have independent y-axis scales?

### Value

An aggregate coverage plot.

### Methods (by class)

- `CompressedRleList`: S3 method for CompressedRleList

- `SimpleRleList`: S3 method for SimpleRleList

- `list`: S3 method for list

### Examples

    data(ce11_ATACseq)
    data(ce11_WW_10bp)
    data(ce11_proms)

    p1 <- plotAggregateCoverage(
        ce11_ATACseq,
        resize(ce11_proms[1:100], fix = 'center', width = 1000)
    )
    p1

    proms <- resize(ce11_proms[1:100], fix = 'center', width = 400)
    p2 <- plotAggregateCoverage(
        ce11_ATACseq,
        list(
            'Ubiq & Germline promoters' =
                proms[proms$which.tissues %in% c('Ubiq.', 'Germline')],
            'Other promoters' =
                proms[!(proms$which.tissues %in% c('Ubiq.', 'Germline'))]
        )
    )
    p2

    p3 <- plotAggregateCoverage(
        list(
            'atac' = ce11_ATACseq,
            'WW_10bp' = ce11_WW_10bp
        ),
        proms,
        norm = 'zscore'
    )
    p3

    p4 <- plotAggregateCoverage(
        list(
            'ATAC-seq' = ce11_ATACseq,
            'WW 10-bp periodicity' = ce11_WW_10bp
        ),
        list(
            'Ubiq & Germline promoters' =
                proms[proms$which.tissues %in% c('Ubiq.', 'Germline')],
            'Other promoters' =
                proms[!(proms$which.tissues %in% c('Ubiq.', 'Germline'))]
        ),
        norm = 'zscore'
    )
    p4

    p5 <- plotAggregateCoverage(
        list(
            'ATAC-seq' = ce11_ATACseq,
            'WW 10-bp periodicity' = ce11_WW_10bp
        ),
        list(
            'Ubiq & Germline promoters' =
                proms[proms$which.tissues %in% c('Ubiq.', 'Germline')],
            'Other promoters' =
                proms[!(proms$which.tissues %in% c('Ubiq.', 'Germline'))]
        ),
        split_by_granges = FALSE,
        split_by_track = TRUE,
        norm = 'zscore'
    )
    p5

[Package periodicDNA version 1.4.0 Index]