plotGcContent {ngsReports} | R Documentation

## Plot the Per Sequence GC Content

### Description

Plot the Per Sequence GC Content for a set of FASTQC files

### Usage

    plotGcContent(x, usePlotly = FALSE, labels, theoreticalGC = TRUE,
      gcType = c("Genome", "Transcriptome"), species = "Hsapiens",
      GCobject, Fastafile, n = 1e+06, ...)

    ## S4 method for signature 'ANY'
    plotGcContent(x, usePlotly = FALSE, labels,
      theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"),
      species = "Hsapiens", GCobject, Fastafile, n = 1e+06, ...)

    ## S4 method for signature 'character'
    plotGcContent(x, usePlotly = FALSE, labels,
      theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"),
      species = "Hsapiens", GCobject, Fastafile, n = 1e+06, ...)

    ## S4 method for signature 'FastqcData'
    plotGcContent(x, usePlotly = FALSE, labels,
      theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"),
      species = "Hsapiens", GCobject, Fastafile, n = 1e+06,
      counts = FALSE, lineCols = c("red", "blue"), ...)

    ## S4 method for signature 'FastqcDataList'
    plotGcContent(x, usePlotly = FALSE, labels,
      theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"),
      species = "Hsapiens", GCobject, Fastafile, n = 1e+06,
      plotType = c("heatmap", "line"), pwfCols, cluster = FALSE,
      dendrogram = FALSE, ...)

### 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.
`theoreticalGC` | `logical` default is `FALSE` to give the true GC content, set to `TRUE` to normalize values of GC_Content by the theoretical values using `gcTheoretical`. `species` must be specified.
`gcType` | `character` Select type of data to normalize GC content against. Accepts either "Genome" (default) or "Transcriptome".
`species` | `character` if `gcTheory` is `TRUE` it must be accompanied by a species. Species currently supported can be obtained using `mData(gcTheoretical)`
`GCobject` | an object of class GCTheoretical. Defaults to the gcTheoretical object supplied with the package
`Fastafile` | a fasta file contains DNA sequences to generate theoretical GC content
`n` | number of simulated reads to generate theoretical GC content from `Fastafile`
`...` | Used to pass various potting parameters to theme.
`counts` | `logical`. Plot the counts from each file if `counts = TRUE`, otherwise frequencies will be plotted. Ignored if calling the function on a FastqcDataList.
`lineCols` | Colors for observed and theoretical GC lines in single plots
`plotType` | Takes values "line" or "heatmap"
`pwfCols` | Object of class `PwfCols` to give colours for pass, warning, and fail values in plot
`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

Makes plots for GC_Content. When applied to a single FastqcData object a simple line plot will be drawn, with Theoretical GC content overlaid if desired.

When applied to multiple FastQC reports, the density at each GC content bin can be shown as a heatmap by setting `theoreticalGC = FALSE`. By default the difference in observed and expected theoretical GC is shown. Species and genome/transcriptome should also be set if utilising the theoretical GC content.

As an alternative to a heatmap, a series of overlaid distributions can be shown by setting `plotType = "line"`.

Can produce a static ggplot2 object or an interactive plotly object.

### Value

A ggplot2 or 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 a FastqcDataList
    plotGcContent(fdl)

    # Plot a single FastqcData object
    plotGcContent(fdl[[1]])

[Package ngsReports version 1.0.1 Index]