R: Plot the Sequence Length Distribution

plotSeqLengthDistn {ngsReports}

R Documentation

Plot the Sequence Length Distribution

Description

Plot the Sequence Length Distribution across one or more FASTQC reports

Usage

plotSeqLengthDistn(x, usePlotly = FALSE, labels, ...)

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

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

## S4 method for signature 'FastqcData'
plotSeqLengthDistn(
  x,
  usePlotly = FALSE,
  labels,
  plotType = c("line", "cumulative"),
  ...,
  expand.x = expansion(0, 0.2)
)

## S4 method for signature 'FastqcDataList'
plotSeqLengthDistn(
  x,
  usePlotly = FALSE,
  labels,
  counts = FALSE,
  plotType = c("heatmap", "line", "cumulative"),
  cluster = FALSE,
  dendrogram = FALSE,
  ...,
  expand.x = expansion(0, 0.2),
  heatCol = inferno(50)
)

Arguments

`x`	Can be a `FastqcData`, `FastqcDataList` or file paths
`usePlotly`	`logical`. Output as ggplot2 or plotly object.
`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.
`...`	Used to pass additional attributes to theme()
`plotType`	`character`. Can only take the values `plotType = "heatmap"` `plotType = "line"` or `plotType = "cumulative"`
`expand.x`	Output from `expansion()` or numeric vector of length 4. Passed to `scale_x_discrete`
`counts`	`logical` Should distributions be shown as counts or frequencies (percentages)
`cluster`	`logical` default `FALSE`. If set to `TRUE`, fastqc data will be clustered using hierarchical clustering
`dendrogram`	`logical` redundant if `cluster` and `usePlotly` are `FALSE`. If both `cluster` and `dendrogram` are specified as `TRUE` then the dendrogram will be displayed.
`heatCol`	The colour scheme for the heatmap

Details

This extracts the Sequence Length Distribution from the supplied object and generates a ggplot2 object, with a set of minimal defaults. The output of this function can be further modified using the standard ggplot2 methods.

A cumulative plot can also be generated to provide guidance for minimum read length in some NGS workflows, by setting plotType = "cumulative". If all libraries have reads of identical lengths, these plots may be less informative.

An alternative interactive plot is available by setting the argument usePlotly = TRUE.

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)

# Plot as a frequency plot using lines
plotSeqLengthDistn(fdl)

# Or plot the cumulative value
plotSeqLengthDistn(fdl, plotType = "cumulative")

[Package ngsReports version 1.4.2 Index]