plotDupLevels-methods: Plot the combined Sequence_Duplication_Levels information
In ngsReports: Load FastqQC reports and other NGS related files

Description Usage Arguments Details Value Examples

Plot the Sequence_Duplication_Levels information for a set of FASTQC reports

plotDupLevels(x, usePlotly = FALSE, labels, pwfCols, ...)

## S4 method for signature 'ANY'
plotDupLevels(x, usePlotly = FALSE, labels, pwfCols, ...)

## S4 method for signature 'character'
plotDupLevels(x, usePlotly = FALSE, labels, pwfCols, ...)

## S4 method for signature 'FastqcData'
plotDupLevels(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  warn = 20,
  fail = 50,
  lineCols = c("red", "blue"),
  ...
)

## S4 method for signature 'FastqcDataList'
plotDupLevels(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  warn = 20,
  fail = 50,
  deduplication = c("pre", "post"),
  plotType = c("heatmap", "line"),
  cluster = FALSE,
  dendrogram = FALSE,
  heatCol = inferno(50),
  ...
)

`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.
`pwfCols`	Object of class `PwfCols` to give colours for pass, warning, and fail values in the plot
`...`	Used to pass additional attributes to theme() and between methods
`warn, fail`	The default values for warn and fail are 20 and 50 respectively (i.e. percentages)
`lineCols`	Colours of the lines drawn for individual libraries
`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` redundant if `cluster` is `FALSE` if both `cluster` and `dendrogram` are specified as `TRUE` then the dendrogram will be displayed.
`heatCol`	Colour palette used for the heatmap

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.

A standard ggplot2 or plotly object

# 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)