plotOverrep {ngsReports} | R Documentation

## Plot a summary of Over-represented Sequences

### Description

Plot a summary of Over-represented Sequences for a set of FASTQC reports

### Usage

    plotOverrep(x, usePlotly = FALSE, labels, pwfCols, ...)

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

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

    ## S4 method for signature 'FastqcData'
    plotOverrep(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      n = 10,
      ...,
      expand.x = expansion(mult = c(0, 0.05)),
      expand.y = expansion(0, 0.6)
    )

    ## S4 method for signature 'FastqcDataList'
    plotOverrep(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      cluster = FALSE,
      dendrogram = FALSE,
      ...,
      paletteName = "Set1",
      expand.x = expansion(mult = c(0, 0.05)),
      expand.y = expansion(0, 0)
    )

### Arguments

`x` | Can be a `FastqcData`, `FastqcDataList` or file paths
`usePlotly` | `logical` Default `FALSE` will render using ggplot. If `TRUE` plot will be rendered with plotly
`labels` | An optional named factor 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
`...` | Used to pass additional attributes to theme() and between methods
`n` | The number of sequences to plot from an individual file
`expand.x, expand.y` | Output from `expansion()` or numeric vectors of length 4. Passed to `scale_*_continuous()`
`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.
`paletteName` | Name of the palette for colouring the possible sources of the overrepresented sequences. Must be a palette name from `RColorBrewer`

### Details

Percentages are obtained by simply summing those within a report. Any possible double counting by FastQC is ignored for the purposes of a simple approximation.

Plots generated from a `FastqcData` object will show the top `n` sequences grouped by their predicted source & coloured by whether the individual sequence would cause a WARN/FAIL.

Plots generated from a `FastqcDataList` group sequences by predicted source and summarise as a percentage of the total reads.

### Value

A standard ggplot2 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)

    # Another example which isn't ideal
    plotOverrep(fdl)

[Package ngsReports version 1.3.2 Index]