plotSeqQuals-methods: Plot the Per Sequence Quality Scores

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

Plot the Per Sequence Quality Scores

Description

Plot the Per Sequence Quality Scores for a set of FASTQC reports

Usage

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

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

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

## S4 method for signature 'FastqcData'
plotSeqQuals(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  showPwf = TRUE,
  counts = FALSE,
  alpha = 0.1,
  warn = 30,
  fail = 20,
  colour = "red",
  plotlyLegend = FALSE,
  ...
)

## S4 method for signature 'FastqcDataList'
plotSeqQuals(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  counts = FALSE,
  alpha = 0.1,
  warn = 30,
  fail = 20,
  showPwf = TRUE,
  plotType = c("heatmap", "line"),
  dendrogram = FALSE,
  cluster = FALSE,
  scaleFill = NULL,
  heatCols = hcl.colors(100, "inferno"),
  heat_w = 8,
  scaleColour = NULL,
  plotlyLegend = FALSE,
  ...
)

Arguments

x	Can be a FastqcData, FastqcDataList or path
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 file names must be present in the names of the vector.
pattern	Regex to remove from the end of any filenames
pwfCols	Object of class PwfCols() containing the colours for PASS/WARN/FAIL
...	Used to pass various potting parameters to theme. Can also be used to set size and colour for box outlines.
showPwf	logical(1) Show PASS/WARN/FAIL status
counts	logical. Plot the counts from each file if counts = TRUE, otherwise the frequencies will be plotted
alpha	set alpha for line graph bounds
warn, fail	The default values for warn and fail are 5 and 10 respectively (i.e. percentages)
colour	Colour for single line plots
plotlyLegend	logical(1) Show legend for interactive line plots
plotType	character. Can only take the values plotType = "heatmap" or plotType = "line"
dendrogram	logical redundant if cluster is FALSE if both cluster and dendrogram are specified as TRUE then the dendrogram will be displayed.
cluster	logical default FALSE. If set to TRUE, fastqc data will be clustered using hierarchical clustering
scaleFill, scaleColour	ggplot2 scales
heatCols	Colour palette for the heatmap
heat_w	Relative width of any heatmap plot components

Details

Plots the distribution of average sequence quality scores across the set of files. Values can be plotted either as counts (counts = TRUE) or as frequencies (counts = FALSE).

Any faceting or scale adjustment can be performed after generation of the initial plot, using the standard methods of ggplot2 as desired.

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
plotSeqQuals(fdl)

# Also subset the reads to just the R1 files
r1 <- grepl("R1", fqName(fdl))
plotSeqQuals(fdl[r1])

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