plotSeqLengthDistn {ngsReports} | R Documentation

## Plot the Sequence Length Distribution

### Description

Plot the Sequence Length Distribution across one or more FASTQC reports

### Usage

    plotSeqLengthDistn(x, usePlotly = FALSE, labels, ...)

    ## S4 method for signature 'ANY'
    plotSeqLengthDistn(x, usePlotly = FALSE, labels, ...)

    ## S4 method for signature 'character'
    plotSeqLengthDistn(x, usePlotly = FALSE, labels, ...)

    ## S4 method for signature 'FastqcData'
    plotSeqLengthDistn(
      x,
      usePlotly = FALSE,
      labels,
      plotType = c("line", "cumulative"),
      ...,
      expand.x = expansion(0, 0.2)
    )

    ## S4 method for signature 'FastqcDataList'
    plotSeqLengthDistn(
      x,
      usePlotly = FALSE,
      labels,
      counts = FALSE,
      plotType = c("heatmap", "line", "cumulative"),
      cluster = FALSE,
      dendrogram = FALSE,
      ...,
      expand.x = expansion(0, 0.2),
      heatCol = inferno(50)
    )

### Arguments

`x` | Can be a `FastqcData`, `FastqcDataList` or file paths
`usePlotly` | `logical`. Output as ggplot2 or plotly object.
`labels` | An optional named vector of labels for the file names. All filenames must be present in the names. File extensions are dropped by default.
`...` | Used to pass additional attributes to theme()
`plotType` | `character`. Can only take the values `plotType = "heatmap"` `plotType = "line"` or `plotType = "cumulative"`
`expand.x` | Output from `expansion()` or numeric vector of length 4. Passed to `scale_x_discrete`
`counts` | `logical` Should distributions be shown as counts or frequencies (percentages)
`cluster` | `logical` default `FALSE`. If set to `TRUE`, fastqc data will be clustered using hierarchical clustering
`dendrogram` | `logical` redundant if `cluster` and `usePlotly` are `FALSE`. If both `cluster` and `dendrogram` are specified as `TRUE` then the dendrogram will be displayed.
`heatCol` | The colour scheme for the heatmap

### Details

This extracts the Sequence Length Distribution from the supplied object and generates a ggplot2 object, with a set of minimal defaults. The output of this function can be further modified using the standard ggplot2 methods.

A cumulative plot can also be generated to provide guidance for minimum read length in some NGS workflows, by setting `plotType = "cumulative"`. If all libraries have reads of identical lengths, these plots may be less informative.

An alternative interactive plot is available by setting the argument `usePlotly = TRUE`.

### Value

A standard ggplot2 object, or an interactive plotly object

### Examples

    # Get the files included with the package
    packageDir <- system.file("extdata", package = "ngsReports")
    fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE)

    # Load the FASTQC data as a FastqcDataList object
    fdl <- FastqcDataList(fl)

    # Plot as a frequency plot using lines
    plotSeqLengthDistn(fdl)

    # Or plot the cumulative value
    plotSeqLengthDistn(fdl, plotType = "cumulative")

[Package ngsReports version 1.3.2 Index]