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Generate the tibble used by the plotting functions

Source: R/visualization.R
ir_generate_tibble.Rd

These helpers build the exact flat tibble that ir_plot_continuous_flow() (ir_generate_traces_tibble()), ir_plot_dual_inlet() (ir_generate_cycles_tibble()), and ir_plot_scans() (ir_generate_scans_tibble()) plot, so it can be inspected or used independently of producing a plot. The dataset is prepared exactly as for the plotting functions (an ir_aggregated_data object has its traces / cycles / scans dataset inner-joined with $metadata; a plain data frame is used as is), filtered by species, and then split into intensity rows and (optionally) ratio rows, each augmented with three columns:

  • trace - the identifier "<species>: <mass>" for intensity rows (e.g. "CO2: 44") or "<species>: <ratio_name>" for ratio rows (e.g. "CO2: 45/44"), always (re)generated and returned as a factor sorted by species and numerical (numerator) mass.

  • data_type - "intensity [UNITS]" (e.g. "intensity [mV]") for the intensity rows, or "ratios" for ratio rows.

  • value - the value to plot: the intensity for intensity rows, or the (optionally fold-clamped) ratio for ratio rows.

Usage

ir_generate_traces_tibble(dataset, species = NULL, mass = NULL, ratio = NULL)

ir_generate_cycles_tibble(dataset, species = NULL, mass = NULL, ratio = NULL)

ir_generate_scans_tibble(dataset, species = NULL, mass = NULL, ratio = NULL)

Arguments

dataset

an ir_aggregated_data object from ir_aggregate_isofiles() or a plain data frame with the required columns (see the matching plotting function)

species

optional vector to filter to specific species (e.g. "CO2" or c("N2", "CO2")); default NULL keeps all species.

mass

which masses to include as intensity traces: NULL (default) for all masses, a vector (e.g. 44 or c(44, 45)) for specific masses, or a zero-length vector (numeric(0)/character(0)) for none. Note that c() is NULL in R, i.e. all masses.

ratio

which ratios to include (computed with ir_calculate_ratios()): NULL (default) for all available ratios, a character vector of ratio names (e.g. c("45/44", "46/44")) for specific ones, or character(0) for none. Requesting specific ratio names when ratios have not been calculated is an error pointing to ir_calculate_ratios(); with ratio = NULL and no ratios present none are simply added.

Value

a tibble with the prepared data plus the trace, data_type, and value columns described above.