plotSeqLengthDistn-methods: Plot the Sequence Length Distribution

In UofABioinformaticsHub/fastqcReports: Load FastqQC reports and other NGS related files

Plot the Sequence Length Distribution

Description

Plot the Sequence Length Distribution across one or more FASTQC reports

Usage

plotSeqLengthDistn(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  ...
)

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

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

## S4 method for signature 'FastqcData'
plotSeqLengthDistn(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  counts = TRUE,
  plotType = c("line", "cdf"),
  expand.x = c(0, 0.2, 0, 0.2),
  plotlyLegend = FALSE,
  colour = "red",
  ...
)

## S4 method for signature 'FastqcDataList'
plotSeqLengthDistn(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  counts = FALSE,
  plotType = c("heatmap", "line", "cdf"),
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8,
  pwfCols,
  showPwf = TRUE,
  scaleFill = NULL,
  scaleColour = NULL,
  heatCol = hcl.colors(50, "inferno"),
  plotlyLegend = FALSE,
  ...
)

Arguments

x	Can be a FastqcData, FastqcDataList or file paths
usePlotly	logical. Output as ggplot2 or plotly object.
labels	An optional named vector of labels for the file names. All filenames must be present in the names.
pattern	Regex to remove from the end of any filenames
...	Used to pass additional attributes to theme()
counts	logical Should distributions be shown as counts or frequencies (percentages)
plotType	character. Can only take the values plotType = "heatmap" plotType = "line" or plotType = "cdf"
expand.x	Output from expansion() or numeric vector of length 4. Passed to scale_x_discrete
plotlyLegend	logical(1) Show legend for interactive line plots
colour	Line colour
cluster	logical default FALSE. If set to TRUE, fastqc data will be clustered using hierarchical clustering
dendrogram	logical redundant if cluster and usePlotly are 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 PASS/WARN/FAIL status
scaleFill, scaleColour	Optional ggplot scale objects
heatCol	The colour scheme for the heatmap

Details

This extracts the Sequence Length Distribution from the supplied object and generates a ggplot2 object, with a set of minimal defaults. The output of this function can be further modified using the standard ggplot2 methods.

A cdf plot can also be generated to provide guidance for minimum read length in some NGS workflows, by setting plotType = "cdf". If all libraries have reads of identical lengths, these plots may be less informative.

An alternative interactive plot is available by setting the argument 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)

# Plot as a frequency plot using lines
plotSeqLengthDistn(fdl)

# Or plot the cdf
plotSeqLengthDistn(fdl, plotType = "cdf")

UofABioinformaticsHub/fastqcReports documentation built on July 23, 2024, 3:26 p.m.