R: Plot the Per Sequence GC Content

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 1.3.2 Index]