Prepare plotting data from continuous flow files

This function helps with the preparation of plotting data from continuous flow data files (i.e. the raw chromatogram data). Call either explicity and pass the result to iso_plot_continuous_flow_data or let iso_plot_continuous_flow_data take care of preparing the plotting data directly from the iso_files. If a peak_table is provided for peak annotation purposes, uses iso_combine_raw_data_with_peak_table to combine the raw data from the iso_files with the provided peak data table.

iso_prepare_continuous_flow_plot_data(
  iso_files,
  data = character(),
  include_file_info = NULL,
  time_interval = c(),
  time_interval_units = "seconds",
  filter = NULL,
  normalize = FALSE,
  zoom = NULL,
  zoom_group = data,
  peak_table = NULL,
  file_id = default(file_id),
  rt = default(rt),
  rt_start = default(rt_start),
  rt_end = default(rt_end),
  rt_unit = NULL
)

Arguments

iso_files	collection of iso_file objects
data	which masses and ratios to plot (e.g. `c("44", "45", "45/44")` - without the units), if omitted, all available masses and ratios are plotted. Note that ratios should be calculated using `iso_calculate_ratios` prior to plotting.
time_interval	which time interval to plot
time_interval_units	which units the time interval is in, default is "seconds"
filter	any filter condition to apply to the data beyond the masses/ratio selection (param `data`) and time interval (param `time_interval`). For details on the available data columns see iso_get_raw_data with parameters `gather = TRUE` and `include_file_info = everything()` (i.e. all file info is available for plotting aesthetics).
normalize	whether to normalize the data (default is FALSE, i.e. no normalization). If TRUE, normalizes each trace across all files (i.e. normalized to the global max/min). This is particularly useful for overlay plotting different mass and/or ratio traces (`panel = NULL`). Note that zooming (if `zoom` is set) is applied after normalizing.
zoom	if not set, automatically scales to the maximum range in the selected time_interval in each plotting panel. If set, scales by the indicated factor, i.e. values > 1 are zoom in, values < 1 are zoom out, baseline always remains the bottom anchor point. Note that zooming is always relative to the max in each zoom_group (by default `zoom_group = data`, i.e. each trace is zoomed separately). The maximum considered may be outside the visible time window. Note that for `zoom_group` other than `data` (e.g. `file_id` or `NULL`), zooming is relative to the max signal across all mass traces. Typically it makes most sense to set the `zoom_group` to the same variable as the planned `panel` parameter to the plotting function. Lastly, note that zooming only affects masses, ratios are never zoomed.
peak_table	a data frame that describes the peaks in this chromatogram. By default, the chromatographic data is prepared WITHOUT peaks information. Supply this parameter to add in the peaks data. Typically via `iso_get_peak_table`. Note that the following parameters must also be set correctly IF `peak_table` is supplied and has non-standard column names: `file_id`, `rt`, `rt_start`, `rt_end`.
file_id	the column (or columns) that uniquely identifies individual analyses for proper matching of the raw chromatography data with the peak_table data. In most cases dealing with isoreader data, the default (`file_id`) should work fine.
rt	the column in the `peak_table` that holds the retention time of the peak.
rt_start	the column in the`peak_table` that holds the retention time where each peak starts.
rt_end	the column in the`peak_table` that holds the retention time where each peak ends.
rt_unit	which time unit the retention time columns (`rt`, `rt_start`, `rt_end`) are in. Only required if the retention time columns are not `iso_double_with_units` columns and are not in the same unit as the time column of the raw data. If provided, will override column units.

Arguments

See also