Plot scan data — ir_plot_scans • isoreader2

Plots scan data from an ir_aggregate_isofiles() result or a plain data frame. When dataset is an ir_aggregated_data object, the $scans dataset is inner-joined with $metadata (bringing in all metadata columns not already present in $scans) before plotting. The plot data must contain x, scan_type, x_units, mass, and an intensity.* column — an error is thrown if any are missing. The intensity unit suffix becomes the y axis label; scan_type and x_units are combined for the x axis label. If mass is not already a factor it is converted to one with levels sorted in numerical order.

Usage

ir_plot_scans(
  dataset,
  scan_type = NULL,
  panel = file_name,
  color = mass,
  linetype = species,
  color_values = palette.colors(),
  scientific = FALSE,
  x_window = NULL,
  n_x_breaks = 5,
  n_y_breaks = 5,
  theme = ir_default_theme()
)

Arguments

dataset: an ir_aggregated_data object from ir_aggregate_isofiles() or a plain data frame with x, scan_type, x_units, mass, and an intensity.* column
scan_type: which scan type to plot (e.g. "high voltage"). Required when the data contains more than one scan type; an error lists the available types. If the data contains only one scan type, the parameter must either be NULL or match that type exactly.
panel: column or expression for faceting (default: file_name). Set to NULL to suppress panels.
color: column or expression for the colour aesthetic (default: mass)
linetype: column or expression for the linetype aesthetic (default: species)
color_values: named or unnamed character vector of colours passed to ggplot2::scale_color_manual(), or NULL to use the ggplot2 default colour palette (default: palette.colors())
scientific: whether to format y axis labels in scientific notation (default: FALSE)
x_window: optional numeric vector of length 2 giving the x axis display window c(min, max). Data just outside the window is retained for correct y autoscaling at the edges; ggplot2::coord_cartesian() clips the display. Default NULL shows the full x range.
n_x_breaks: desired number of x axis tick marks (default: 5)
n_y_breaks: desired number of y axis tick marks (default: 5)
theme: ggplot2 theme to apply (default: ir_default_theme())

Value

a ggplot object