plot.scSpectra {MALDIrppa} | R Documentation |
screenSpectra
objects
This is a plot
method for scSpectra
objects that displays the results from applying screenSpectra
to identify potential faulty, low-quality raw mass spectra.
## S3 method for class 'scSpectra' plot(x, type = c("index", "hist", "casewise"), breaks = 30, labels = FALSE, col = "green3", ...)
x |
A |
type |
Type of graphical display. |
breaks |
Number of break points for plotting a histogram when |
labels |
Vector of labels for the mass spectra (default = |
col |
Colour for the histogram bars when |
... |
Other arguments. |
For type = "index"
(default) the upper and lower fences used to declare a mass spectrum as potentially low-quality are shown along with their A scores (see screenSpectra
for details). Point labels can be added using the labels
argument (either a position index when labels = TRUE
or a given vector of labels; see examples below). For type = "hist"
a histogram of the distribution of the A scores is produced along with the tolerance fences. Finally, type = "casewise"
displays interactively the flagged spectra for visual inspection.
No return value, graphical output.
See screenSpectra
and summary.scSpectra
.
# Load example data data(spectra) # list of MassSpectra objects data(type) # metadata sc.results <- screenSpectra(spectra) plot(sc.results) plot(sc.results, labels = TRUE) plot(sc.results, labels = type$SpectID) plot(sc.results, type = "hist")