plotSummary {ngsReports} | R Documentation |
Extract the PASS/WARN/FAIL summaries and plot them
plotSummary(x, usePlotly = FALSE, labels, pwfCols, cluster = FALSE, dendrogram = FALSE, ...) ## S4 method for signature 'ANY' plotSummary(x, usePlotly = FALSE, labels, pwfCols, cluster = FALSE, dendrogram = FALSE, ...) ## S4 method for signature 'character' plotSummary(x, usePlotly = FALSE, labels, pwfCols, cluster = FALSE, dendrogram = FALSE, ...) ## S4 method for signature 'FastqcDataList' plotSummary(x, usePlotly = FALSE, labels, pwfCols, cluster = FALSE, dendrogram = FALSE, ..., gridlineWidth = 0.2, gridlineCol = "grey20")
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 |
cluster |
|
dendrogram |
|
... |
Used to pass various potting parameters to theme. |
gridlineWidth, gridlineCol |
Passed to geom_hline and geom_vline to determine width and colour of gridlines |
This uses the standard ggplot2 syntax to create a three colour plot. The output of this function can be further modified using the standard ggplot2 methods if required.
A ggplot2 object (usePlotly = FALSE
)
or an interactive plotly object (usePlotly = TRUE
)
# 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) # Check the overall PASS/WARN/FAIL status plotSummary(fdl)