Plot the Per Sequence Quality Scores

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

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

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

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

# S4 method for class '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 class '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

Value

A standard ggplot2 object, or an interactive plotly object

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.

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])