plotGcContent-methods: Plot the Per Sequence GC Content

In steveped/ngsReports: Load FastqQC reports and other NGS related files

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, pattern = ".(fast|fq|bam).*", ...)

## S4 method for signature 'ANY'
plotGcContent(x, usePlotly = FALSE, labels, pattern = ".(fast|fq|bam).*", ...)

## S4 method for signature 'FastqcData'
plotGcContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  theoreticalGC = TRUE,
  gcType = c("Genome", "Transcriptome"),
  species = "Hsapiens",
  GCobject,
  plotlyLegend = FALSE,
  Fastafile,
  n = 1e+06,
  counts = FALSE,
  scaleColour = NULL,
  lineCols = c("red3", "black"),
  linetype = 1,
  linewidth = 0.5,
  ...
)

## S4 method for signature 'FastqcDataList'
plotGcContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  theoreticalGC = TRUE,
  gcType = c("Genome", "Transcriptome"),
  species = "Hsapiens",
  GCobject,
  Fastafile,
  n = 1e+06,
  plotType = c("heatmap", "line", "cdf"),
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8,
  pwfCols,
  showPwf = TRUE,
  scaleFill = NULL,
  scaleColour = NULL,
  plotlyLegend = FALSE,
  lineCols = RColorBrewer::brewer.pal(12, "Paired"),
  linetype = 1,
  linewidth = 0.5,
  ...
)

## S4 method for signature 'FastpData'
plotGcContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  theoreticalGC = TRUE,
  gcType = c("Genome", "Transcriptome"),
  species = "Hsapiens",
  GCobject,
  Fastafile,
  n = 1e+06,
  plotType = "bar",
  scaleFill = NULL,
  plotlyLegend = FALSE,
  plotTheme = theme_get(),
  ...
)

## S4 method for signature 'FastpDataList'
plotGcContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  theoreticalGC = TRUE,
  gcType = c("Genome", "Transcriptome"),
  species = "Hsapiens",
  GCobject,
  Fastafile,
  n = 1e+06,
  plotType = "bar",
  scaleFill = NULL,
  plotTheme = theme_get(),
  plotlyLegend = 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.
pattern	Pattern to remove from the end of filenames
...	Used to pass various potting parameters to themes and geoms.
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. For Fastqc* objects, the entire distributions will be used, wheras for the Fastp* objects, only the expected mean value is shown as a horizontal line
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
plotlyLegend	logical(1) Show legend on interactive line plots
Fastafile	a fasta file contains DNA sequences to generate theoretical GC content
n	number of simulated reads to generate theoretical GC content from Fastafile
counts	logical. Plot the counts from each file if counts = TRUE, otherwise frequencies will be plotted. Ignored if calling the function on a FastqcDataList.
scaleColour	ggplot2 scale for line colours
lineCols, linetype, linewidth	Line colour type and width for observed and theoretical GC lines
plotType	Takes values "line", "heatmap" or "cdf"
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.
heat_w	Relative width of any heatmap plot components
pwfCols	Object of class PwfCols() to give colours for pass, warning, and fail values in plot
showPwf	logical(1) Show Pwf Status on the plot
scaleFill	ggplot2 scale for filling heatmap cells or bars
plotTheme	theme object

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]])

steveped/ngsReports documentation built on July 24, 2024, 10:45 a.m.