plotSeqContent {ngsReports} | R Documentation |
Plot the Per Base content for a set of FASTQC files.
plotSeqContent(x, usePlotly = FALSE, labels, ...) ## S4 method for signature 'ANY' plotSeqContent(x, usePlotly = FALSE, labels, ...) ## S4 method for signature 'character' plotSeqContent(x, usePlotly = FALSE, labels, ...) ## S4 method for signature 'FastqcData' plotSeqContent(x, usePlotly = FALSE, labels, ...) ## S4 method for signature 'FastqcDataList' plotSeqContent( x, usePlotly = FALSE, labels, pwfCols, plotType = c("heatmap", "line", "residuals"), cluster = FALSE, dendrogram = FALSE, ..., nc = 2 )
x |
Can be a |
usePlotly |
|
labels |
An optional named vector of labels for the file names. All file names must be present in the names of the vector. File extensions are dropped by default. |
... |
Used to pass additional attributes to theme() and between methods |
pwfCols |
Object of class |
plotType |
|
cluster |
|
dendrogram |
|
nc |
Specify the number of columns if plotting a FastqcDataList as line
plots. Passed to |
Per base sequence content (
heatmap colours when plotting from multiple reports. The individual line
plots are able to be generated by setting plotType = "line"
, and the
layout is determined by facet_wrap
from ggplot2.
Individual line plots are also generated when plotting from a single
FastqcData
object.
If setting usePlotly = TRUE
for a large number of reports, the plot
can be slow to render.
An alternative may be to produce a plot of residuals for each base, produced
by taking the position-specific mean for each base.
A 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 plotSeqContent(fdl)