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.

iso_prepare_continuous_flow_plot_data(iso_files, data = c(),
  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. Note that the following parameters must also be set correctly IF peak_table is supplied: file_id, rt, rt_start, rt_end.

file_id

the column (or columns) that uniquely identify each iso_file for proper matching of the raw chromatography data with the peak_table data. In most cases, 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 thepeak_table that holds the retention time where each peak starts.

rt_end

the column in thepeak_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. If not specified (i.e. the default), assumes it is the same unit as the time column of the iso_files raw data.

See also