Plot continuous flow data — ir_plot_continuous

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

Usage

ir_plot_continuous_flow(
  dataset,
  panel = file_name,
  color = mass,
  linetype = species,
  color_values = palette.colors(),
  scientific = FALSE,
  time_window = NULL,
  short_time_labels = FALSE,
  n_time_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 time.s, mass, and an intensity.* column
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)
time_window: optional numeric vector of length 2 giving the time axis display window c(min, max) in seconds. 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 time range.
short_time_labels: whether to use compact time axis labels with no space between value and unit and abbreviated units (hr, m, s) (default: FALSE)
n_time_breaks: desired number of time 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