Plot GC/MS signals, compound profiles and recovered spectra

Draw four signal heatmaps, background-corrected observed mass traces with fitted compound profiles, or recovered mass spectra. Observations are read from the source CDF for the requested interval and released after plotting.

Usage

# S3 method for class 'GCMSdeco'
plot(
  x,
  type = c("lines", "heatmap", "spectra", "profiles"),
  file = NULL,
  time_range = NULL,
  mass = NULL,
  which = NULL,
  nrows = 4L,
  ncols = 2L,
  minutes_per_panel = 2.5,
  transform = c("sqrt", "identity", "log1p"),
  peak_scale = c("basepeak", "total"),
  labels = FALSE,
  max_time = 1600L,
  clip = 0.999,
  gamma = 0.13,
  residual_limit = 3,
  order = c("rt", "area", "height", "index"),
  ...
)

Arguments

x: A fitted GCMSdeco() object.
type: "lines", "heatmap", "spectra" or "profiles". The last places each compound's total-ion profile beside its spectrum, with one compound per row.
file: Optional PDF output path. NULL uses the current device. PDF reports can contain multiple pages.
time_range: Retention-time bounds in minutes; NULL uses the full fitted interval.
mass: Optional vector of recorded nominal m/z values.
which: Compound indices, as returned in x$compounds$compound. NULL shows all compounds.
nrows, ncols: Rows per PDF page, and columns for spectral panels. Profile-and-spectrum panels always use two columns.
minutes_per_panel: Retention-time span of each line panel, default 2.5 minutes. Consecutive panels cover the whole selected interval.
transform: Line-display transform: signed square root (default), identity or signed log1p. Negative background-corrected traces are retained. Tick labels use the original intensity scale.
peak_scale: "basepeak" scales each profile by its strongest ion in the displayed mass range, matching the individual grey mass traces. "total" uses the compound's summed ion intensity and shows the observed total ion trace in grey.
labels: Label line-profile apices by compound index.
max_time: Maximum heatmap time bins. Data and fitted signals are averaged over the same bins, retaining all selected mass channels.
clip: Upper quantile used for heatmap colour saturation, default .999. Set to one to display the full transformed range.
gamma: Positive heatmap contrast exponent, default .13 as in plotmat().
residual_limit: Symmetric Pearson-residual colour limit, default 3.
order: Spectral panel order: "rt" (default) uses increasing apex retention time; "area" or "height" uses decreasing compound area or total-ion peak height; "index" preserves the selected indices.
...: Graphical arguments passed to the line or spectral panel.

Value

Invisibly, x. Plotting does not attach observed data to it.

Details

Heatmaps show the observed signal, observed signal minus modeled background, fitted chromatogram and Pearson residuals. Spline background and any known offset are subtracted in the second heatmap and grey line traces. Signal heatmaps use the plotmat() black-blue-green-yellow-orange-red palette and truncate negative corrected intensities at zero. Pearson residuals use blue-black-red for negative-zero-positive deviations, without an intensity transform. Display time bins contain their average residual. Heatmaps are interpolated onto a regular display grid and drawn as rasters; red vertical lines mark the selected compound apices. Spectral panels use base-peak percentages. The Excel compound sheet places a compact spectrum beside the integrated area; coef(x,normalize="l1") returns unit-L1 spectra.

Examples

if (FALSE) { # \dontrun{
fit <- GCMSdeco("beer.cdf", "beer.msp", xlsx_file="beer.xlsx")
plot(fit, type="heatmap", file="beer_heatmaps.pdf")
plot(fit, type="lines", file="beer_traces.pdf", minutes_per_panel=2.5)
plot(fit, type="spectra", file="beer_spectra.pdf",
     which=head(fit$compounds$compound[order(-fit$compounds$area)],24))
} # }