plotDupLevels-methods: Plot the combined Sequence_Duplication_Levels information

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

Plot the combined Sequence_Duplication_Levels information

Description

Plot the Sequence_Duplication_Levels information for a set of FASTQC reports

Usage

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

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

## S4 method for signature 'FastqcData'
plotDupLevels(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 20,
  fail = 50,
  showPwf = TRUE,
  plotlyLegend = FALSE,
  lineCol = c("red", "blue"),
  lineWidth = 1,
  ...
)

## S4 method for signature 'FastqcDataList'
plotDupLevels(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 20,
  fail = 50,
  showPwf = TRUE,
  plotlyLegend = FALSE,
  deduplication = c("pre", "post"),
  plotType = c("heatmap", "line"),
  cluster = FALSE,
  dendrogram = FALSE,
  heatCol = hcl.colors(50, "inferno"),
  heat_w = 8,
  ...
)

## S4 method for signature 'FastpData'
plotDupLevels(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 20,
  fail = 50,
  showPwf = FALSE,
  maxLevel = 10,
  lineCol = "red",
  barFill = "dodgerblue4",
  barCol = barFill,
  plotlyLegend = FALSE,
  plotTheme = theme_get(),
  ...
)

## S4 method for signature 'FastpDataList'
plotDupLevels(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 20,
  fail = 50,
  showPwf = FALSE,
  plotlyLegend = FALSE,
  plotType = c("bar", "heatmap"),
  barFill = "blue",
  barCol = "blue",
  cluster = FALSE,
  dendrogram = FALSE,
  scaleFill = NULL,
  plotTheme = theme_get(),
  heat_w = 8,
  maxLevel = 10,
  ...
)

Arguments

x	Can be a FastqcData, FastqcDataList or file 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 filenames must be present in the names. File extensions are dropped by default.
pattern	regex to remove from the end of fastp & fastq file names
...	Used to pass additional attributes to theme() and between methods
pwfCols	Object of class PwfCols() to give colours for pass, warning, and fail values in the plot
warn, fail	The default values for warn and fail are 20 and 50 respectively (i.e. percentages)
showPwf	logical(1) Show PWF rectangles in the background
plotlyLegend	logical(1) Show legend for line plots when using interactive plots
lineCol, lineWidth	Colours and width of lines drawn
deduplication	Plot Duplication levels 'pre' or 'post' deduplication. Can only take values "pre" and "post"
plotType	Choose between "heatmap" and "line"
cluster	logical default FALSE. If set to TRUE, fastqc data will be clustered using hierarchical clustering
dendrogram	logical Plot will automatically be clustered if TRUE.
heatCol	Colour palette used for the heatmap
heat_w	Relative width of the heatmap relative to other plot components
maxLevel	The maximum duplication level to plot. Beyond this level, all values will be summed
barFill, barCol	Colours for bars when calling geom_col()
plotTheme	theme object. Applied after a call to theme_bw()
scaleFill	Discrete scale used to fill heatmap cells

Details

This extracts the Sequence_Duplication_Levels from the supplied object and generates a ggplot2 object, with a set of minimal defaults. For multiple reports, this defaults to a heatmap with block sizes proportional to the percentage of reads belonging to that duplication category.

If setting usePlotly = FALSE, the output of this function can be further modified using standard ggplot2 syntax. If setting usePlotly = TRUE an interactive plotly object will be produced.

Value

A standard 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)

# Draw the default plot for a single file
plotDupLevels(fdl[[1]])

plotDupLevels(fdl)

UofABioinformaticsHub/fastqcReports documentation built on May 8, 2024, 12:44 p.m.