plotNContent {ngsReports} | R Documentation |
Draw an N Content Plot across one or more FastQC reports
plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...) ## S4 method for signature 'ANY' plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...) ## S4 method for signature 'character' plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...) ## S4 method for signature 'FastqcData' plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ..., lineCol = "red") ## S4 method for signature 'FastqcDataList' plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, cluster = FALSE, dendrogram = FALSE, ...)
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 |
pwfCols |
Object of class |
warn, fail |
The default values for warn and fail are 5 and 10 respectively (i.e. percentages) |
... |
Used to pass additional attributes to theme() and between methods |
lineCol |
Defaults to red |
cluster |
|
dendrogram |
|
This extracts the N_Content 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.
When x
is a single FastqcData object line plots will always be drawn
for all Ns.
Otherwise, users can select line plots or heatmaps.
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 plotNContent(fdl[[1]])