plot.scSpectra: Graphical summary of `screenSpectra` objects

Description

This is a plot method for scSpectra objects that displays the results from applying screenSpectra to identify potential faulty, low-quality raw mass spectra.

Usage

# S3 method for scSpectra
plot(x, type = c("index", "hist", "casewise"), breaks = 30,
        labels = FALSE, col = "green3", ...)

Value

No return value, graphical output.

Arguments

x: A scSpectra object as generated by screenSpectra.
type: Type of graphical display.
breaks: Number of break points for plotting a histogram when type = "hist" (default = 30).
labels: Vector of labels for the mass spectra (default = FALSE, no labels).
col: Colour for the histogram bars when type = "hist".
...: Other arguments.

Details

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.

Examples

Run this code

# 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")