plotSeqQuals {ngsReports} | R Documentation |
Plot the Per Sequence Quality Scores for a set of FASTQC reports
plotSeqQuals( x, usePlotly = FALSE, labels, pwfCols, counts = FALSE, alpha = 0.1, warn = 30, fail = 20, ... ) ## S4 method for signature 'ANY' plotSeqQuals( x, usePlotly = FALSE, labels, pwfCols, counts = FALSE, alpha = 0.1, warn = 30, fail = 20, ... ) ## S4 method for signature 'character' plotSeqQuals( x, usePlotly = FALSE, labels, pwfCols, counts = FALSE, alpha = 0.1, warn = 30, fail = 20, ... ) ## S4 method for signature 'FastqcData' plotSeqQuals( x, usePlotly = FALSE, labels, pwfCols, counts = FALSE, alpha = 0.1, warn = 30, fail = 20, ... ) ## S4 method for signature 'FastqcDataList' plotSeqQuals( x, usePlotly = FALSE, labels, pwfCols, counts = FALSE, alpha = 0.1, warn = 30, fail = 20, plotType = c("heatmap", "line"), dendrogram = FALSE, cluster = FALSE, heatCols = hcl.colors(100, "inferno"), ... )
x |
Can be a |
usePlotly |
|
labels |
An optional named factor of labels for the file names. All filenames must be present in the names. File extensions are dropped by default. |
pwfCols |
Object of class |
counts |
|
alpha |
set alpha for line graph bounds |
warn, fail |
The default values for warn and fail are 5 and 10 respectively (i.e. percentages) |
... |
Used to pass various potting parameters to theme. Can also be used to set size and colour for box outlines. |
plotType |
|
dendrogram |
|
cluster |
|
heatCols |
Colour palette for the heatmap |
Plots the distribution of average sequence quality scores across the
set of files. Values can be plotted either as counts (counts = TRUE
)
or as frequencies (counts = FALSE
).
Any faceting or scale adjustment can be performed after generation of the initial plot, using the standard methods of ggplot2 as desired.
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) # The default plot plotSeqQuals(fdl) # Also subset the reads to just the R1 files r1 <- grepl("R1", fqName(fdl)) plotSeqQuals(fdl[r1])