plotOverrep {ngsReports} | R Documentation |
Plot a summary of Over-represented Sequences for a set of FASTQC reports
plotOverrep(x, usePlotly = FALSE, labels, pwfCols, ...) ## S4 method for signature 'ANY' plotOverrep(x, usePlotly = FALSE, labels, pwfCols, ...) ## S4 method for signature 'character' plotOverrep(x, usePlotly = FALSE, labels, pwfCols, ...) ## S4 method for signature 'FastqcData' plotOverrep(x, usePlotly = FALSE, labels, pwfCols, n = 10, ..., expand.x = expand_scale(mult = c(0, 0.05)), expand.y = expand_scale(0, 0.6)) ## S4 method for signature 'FastqcDataList' plotOverrep(x, usePlotly = FALSE, labels, pwfCols, cluster = TRUE, dendrogram = TRUE, ..., paletteName = "Set1", expand.x = expand_scale(mult = c(0, 0.05)), expand.y = expand_scale(0, 0))
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 |
... |
Used to pass additional attributes to theme() and between methods |
n |
The number of sequences to plot from an individual file |
expand.x, expand.y |
Output from |
cluster |
|
dendrogram |
|
paletteName |
Name of the palette for colouring the possible sources
of the overrepresented sequences. Must be a palette name from
|
Percentages are obtained by simply summing those within a report. Any possible double counting by FastQC is ignored for the purposes of a simple approximation.
Plots generated from a FastqcData
object will show the top n
sequences grouped by their predicted source & coloured by whether the
individual sequence would cause a WARN/FAIL.
Plots generated from a FastqcDataList
group sequences by predicted
source and summarise as a percentage of the total reads.
A standard ggplot2 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) # Another example which isn't ideal plotOverrep(fdl)