Topographical plot of a GCIMSSample object

Topographical plot of a GCIMSSample object

# S4 method for class 'GCIMSSample,ANY'
plot(
  x,
  dt_range = NULL,
  rt_range = NULL,
  ...,
  remove_baseline = FALSE,
  trans = "cubic_root",
  intensity_range = "ranged"
)

Arguments

x

A GCIMSSample object

dt_range

A numeric vector of length 2 with the drift time range to plot (in milliseconds)

rt_range

A numeric vector of length 2 with the retention time range to plot (in seconds)

...

Ignored

remove_baseline

Set to TRUE to subtract the estimated baseline first

trans

The transformation to the intensity values. "cubic_root" is the default. "intensity" is also valid. See the trans argument in ggplot2::continuous_scale() for other possibilities.

intensity_range

Controls the color scale limits. One of:

  • "ranged" (the default): the range of exactly what's plotted (respecting dt_range, rt_range and remove_baseline).

  • "global": this sample's own full, uncropped intensity range, regardless of dt_range/rt_range – useful to see how strong a cropped region is relative to the whole sample. With remove_baseline = TRUE, this is the full, uncropped, baseline-removed range.

  • A numeric vector of length 2, c(min, max): fixed limits. Set this explicitly to make several plots comparable on the same color scale.

  • A length-2 vector/list whose elements are independently a number, "global" or "ranged", e.g. list(min = 0, max = "global").

Value

A plot of the GCIMSSample

Examples

dummy_obj <-GCIMSSample(
  drift_time = 1:2,
  retention_time = 1:3,
  data = matrix(1:6, nrow = 2, ncol = 3),
  gc_column = "Optional column name",
  drift_gas = "nitrogen",
  drift_tube_length = 98.0 # in mm
)
plot(dummy_obj)