plotNContent {ngsReports} | R Documentation

## Draw an N Content Plot

### Description

Draw an N Content Plot across one or more FastQC reports

### Usage

    plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...)

    ## S4 method for signature 'ANY'
    plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...)

    ## S4 method for signature 'character'
    plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...)

    ## S4 method for signature 'FastqcData'
    plotNContent(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      warn = 5,
      fail = 20,
      ...,
      lineCol = "red"
    )

    ## S4 method for signature 'FastqcDataList'
    plotNContent(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      warn = 5,
      fail = 20,
      cluster = FALSE,
      dendrogram = FALSE,
      ...
    )

### Arguments

`x` | Can be a `FastqcData`, `FastqcDataList` or file paths
`usePlotly` | `logical`. Output as ggplot2 (default) 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
`pwfCols` | Object of class `PwfCols` containing the colours for PASS/WARN/FAIL
`warn, fail` | The default values for warn and fail are 5 and 10 respectively (i.e. percentages)
`...` | Used to pass additional attributes to theme() and between methods
`lineCol` | Defaults to red
`cluster` | `logical` default `FALSE`. If set to `TRUE`, fastqc data will be clustered using hierarchical clustering
`dendrogram` | `logical` redundant if `cluster` is `FALSE` if both `cluster` and `dendrogram` are specified as `TRUE` then the dendrogram will be displayed.

### Details

This extracts the N_Content 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.

When `x` is a single FastqcData object line plots will always be drawn for all Ns. Otherwise, users can select line plots or heatmaps.

### 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)

    # The default plot
    plotNContent(fdl[[1]])

[Package ngsReports version 1.4.2 Index]