Plot the combined Sequence_Duplication_Levels information

Plot the Sequence_Duplication_Levels information for a set of FASTQC reports

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

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

# S4 method for class '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 class '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 class '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 class '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

Value

A standard ggplot2 or plotly object

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.

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)