plotSeqLengthDistn {ngsReports} | R Documentation |
Plot the Sequence Length Distribution across one or more FASTQC reports
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", "cdf"), ..., expand.x = expansion(0, 0.2) ) ## S4 method for signature 'FastqcDataList' plotSeqLengthDistn( x, usePlotly = FALSE, labels, counts = FALSE, plotType = c("heatmap", "line", "cdf"), cluster = FALSE, dendrogram = FALSE, ..., expand.x = expansion(0, 0.2), heatCol = inferno(50) )
x |
Can be a |
usePlotly |
|
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 |
|
expand.x |
Output from |
counts |
|
cluster |
|
dendrogram |
|
heatCol |
The colour scheme for the heatmap |
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 cdf plot can also be generated to provide guidance for minimum
read length in some NGS workflows, by setting plotType = "cdf"
.
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
.
A standard ggplot2 object, or an interactive 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) # Plot as a frequency plot using lines plotSeqLengthDistn(fdl) # Or plot the cdf plotSeqLengthDistn(fdl, plotType = "cdf")