plotSeqQuals {ngsReports} | R Documentation

## Plot the Per Sequence Quality Scores

### Description

Plot the Per Sequence Quality Scores for a set of FASTQC reports

### Usage

    plotSeqQuals(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      counts = FALSE,
      alpha = 0.1,
      warn = 30,
      fail = 20,
      ...
    )

    ## S4 method for signature 'ANY'
    plotSeqQuals(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      counts = FALSE,
      alpha = 0.1,
      warn = 30,
      fail = 20,
      ...
    )

    ## S4 method for signature 'character'
    plotSeqQuals(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      counts = FALSE,
      alpha = 0.1,
      warn = 30,
      fail = 20,
      ...
    )

    ## S4 method for signature 'FastqcData'
    plotSeqQuals(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      counts = FALSE,
      alpha = 0.1,
      warn = 30,
      fail = 20,
      ...
    )

    ## S4 method for signature 'FastqcDataList'
    plotSeqQuals(
      x,
      usePlotly = FALSE,
      labels,
      pwfCols,
      counts = FALSE,
      alpha = 0.1,
      warn = 30,
      fail = 20,
      plotType = c("heatmap", "line"),
      dendrogram = FALSE,
      cluster = FALSE,
      heatCols = hcl.colors(100, "inferno"),
      ...
    )

### Arguments

`x` | Can be a `FastqcData`, `FastqcDataList` or path
`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
`counts` | `logical`. Plot the counts from each file if `counts = TRUE`, otherwise the frequencies will be plotted
`alpha` | set alpha for line graph bounds
`warn, fail` | The default values for warn and fail are 5 and 10 respectively (i.e. percentages)
`...` | Used to pass various potting parameters to theme. Can also be used to set size and colour for box outlines.
`plotType` | `character`. Can only take the values `plotType = "heatmap"` or `plotType = "line"`
`dendrogram` | `logical` redundant if `cluster` is `FALSE` if both `cluster` and `dendrogram` are specified as `TRUE` then the dendrogram will be displayed.
`cluster` | `logical` default `FALSE`. If set to `TRUE`, fastqc data will be clustered using hierarchical clustering
`heatCols` | Colour palette for the heatmap

### Details

Plots the distribution of average sequence quality scores across the set of files. Values can be plotted either as counts (`counts = TRUE`) or as frequencies (`counts = FALSE`).

Any faceting or scale adjustment can be performed after generation of the initial plot, using the standard methods of ggplot2 as desired.

### 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
    plotSeqQuals(fdl)

    # Also subset the reads to just the R1 files
    r1 <- grepl("R1", fqName(fdl))
    plotSeqQuals(fdl[r1])

[Package ngsReports version 1.10.0 Index]