plotBaseQuals {ngsReports} | R Documentation

## Plot the Base Qualities for each file

### Description

Plot the Base Qualities for each file as separate plots

### Usage

    plotBaseQuals(x, usePlotly = FALSE, labels, pwfCols, warn = 25,
      fail = 20, boxWidth = 0.8, ...)

    ## S4 method for signature 'ANY'
    plotBaseQuals(x, usePlotly = FALSE, labels, pwfCols,
      warn = 25, fail = 20, boxWidth = 0.8, ...)

    ## S4 method for signature 'character'
    plotBaseQuals(x, usePlotly = FALSE, labels,
      pwfCols, warn = 25, fail = 20, boxWidth = 0.8, ...)

    ## S4 method for signature 'FastqcData'
    plotBaseQuals(x, usePlotly = FALSE, labels,
      pwfCols, warn = 25, fail = 20, boxWidth = 0.8, ...)

    ## S4 method for signature 'FastqcDataList'
    plotBaseQuals(x, usePlotly = FALSE, labels,
      pwfCols, warn = 25, fail = 20, boxWidth = 0.8,
      plotType = c("heatmap", "boxplot"), plotValue = "Mean",
      cluster = FALSE, dendrogram = FALSE, nc = 2, ...)

### Arguments

`x` | Can be a `FastqcData`, `FastqcDataList` or character vector of file paths
`usePlotly` | `logical` Default `FALSE` will render using ggplot. If `TRUE` plot will be rendered with plotly
`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` to give colours for pass, warning, and fail values in plot
`warn, fail` | The default values for warn and fail are 30 and 20 respectively (i.e. percentages)
`boxWidth` | set the width of boxes when using a boxplot
`...` | Used to pass additional attributes to theme() and between methods
`plotType` | `character` Can be either `"boxplot"` or `"heatmap"`
`plotValue` | `character` Type of data to be presented. Can be any of the columns returned by `getModule(x, module = "Per_base_sequence_qual")`
`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.
`nc` | `numeric`. The number of columns to create in the plot layout. Only used if drawing boxplots for multiple files in a FastqcDataList

### Details

When acting on a `FastqcDataList`, this defaults to a heatmap using the mean Per_base_sequence_quality score. A set of plots which replicate those obtained through a standard FastQC html report can be obtained by setting `plotType = "boxplot"`, which uses `facet_wrap` to provide the layout as a single ggplot object.

When acting an a `FastqcData` object, this replicates the `Per base sequence quality` plots from FastQC with no faceting.

For large datasets, subsetting by R1 or R2 reads may be helpful.

An interactive plot can be obtained by setting `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)

    # The default plot for multiple libraries is a heatmap
    plotBaseQuals(fdl)

    # The default plot for a single library is the standard boxplot
    plotBaseQuals(fdl[[1]])

[Package ngsReports version 1.0.1 Index]