This function provides easy plotting for mass and ratio chromatograms from continuous flow IRMS data. It can be called either directly with a set of iso_file objects, or with a data frame prepared for plotting chromatographic data (see iso_prepare_continuous_flow_plot_data).

iso_plot_continuous_flow_data(...)

# S3 method for iso_file_list
iso_plot_continuous_flow_data(
iso_files,
data = character(),
time_interval = c(),
time_interval_units = "seconds",
filter = NULL,
normalize = FALSE,
zoom = NULL,
panel = data,
color = file_id,
linetype = NULL,
label = file_id,
peak_table = iso_get_peak_table(iso_files, quiet = TRUE),
file_id = default(file_id),
rt = default(rt),
rt_start = default(rt_start),
rt_end = default(rt_end),
rt_unit = NULL,
peak_marker = FALSE,
peak_bounds = FALSE,
peak_bgrd = FALSE,
peak_label = NULL,
peak_label_filter = NULL,
peak_label_options = list(size = peak_label_size, force = peak_label_repel),
peak_label_size = 2,
peak_label_repel = 1
)

# S3 method for data.frame
iso_plot_continuous_flow_data(
df,
panel = data,
color = file_id,
linetype = NULL,
label = file_id,
peak_marker = FALSE,
peak_bounds = FALSE,
peak_bgrd = FALSE,
peak_label = NULL,
peak_label_filter = NULL,
peak_label_options = list(size = peak_label_size, force = peak_label_repel),
peak_label_size = 2,
peak_label_repel = 1
)

## Arguments

... S3 method placeholder parameters, see class specific functions for details on parameters collection of iso_file objects 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. which time interval to plot which units the time interval is in, default is "seconds" 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). 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. 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. whether to panel plot by anything - any column or complex expression is possible (see notes in the filter parameter for available raw data columns and iso_get_file_info for available file info columns) but the most commonly used options are panel = NULL (overlay all), panel = data (by mass/ratio data), panel = file_id (panel by files, alternatively use any appropriate file_info column or expression that's unique for each file). The default is panelling by the data column. whether to color plot by anything, options are the same as for panel but the default is file_id whether to differentiate by linetype, options are the same as for panel but the default is NULL (i.e. no linetype aesthetic). Note that a limited number of linetypes (6) is defined by default and the plot will fail if a higher number is required unless specified using scale_linetype. this is primarily of use for turning the generated ggplots into interactive plots via ggplotly as the label will be rendered as an additional mousover label. Any unique file identifier is a useful choice, the default is file_id. a data frame that describes the peaks in this chromatogram. By default, the peak table from the iso_files is used if any peak features are requested in the plot (e.g. peak_marker=TRUE or peak_bounds=TRUE). If peak_table is supplied with non-standard column names, the following parameters must also be set correctly: file_id, rt, rt_start, rt_end, and potentially rt_unit. 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. the column in the peak_table that holds the retention time of the peak. the column in thepeak_table that holds the retention time where each peak starts. the column in thepeak_table that holds the retention time where each peak ends. 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. whether to mark identified peaks with a vertical line at the peak retention time. Only works if a peak_table was provided to identify the peaks and will issue a warning if peak_marker = TRUE but no peaks were identified. whether to mark the boundaries of identified peaks with a vertical line at peak start and end retention times. Only works if a peak_table was provided to identify the peaks and will issue a warning if peak_bounds = TRUE but no peaks were identified. NOT YET IMPLEMENTED whether to show the background of identified peaks from start to end retention times. Only works if a peak_table was provided that has bgrdX_start and bgrdX_end columns in the same units as the raw data. whether to label identified peaks. Any valid column or complex expression is supported and ALL columns in the provided peak_table can be used in this expression. The easiest way to generate well constructed peak labels is via the iso_format function. To provide more space for peak labels, it is sometimes useful to use a zoom value smaller than 1 to zoom out a bit, e.g. zoom = 0.9. If peak labels overlap, consider changing peak_label_size and/or peak_label_repel. Note that this only works if a peak_table was provided to identify the peaks and will issue a warning if peak_label is set but no peaks were identified. Also note that peaks whose value at the peak retention time is not visible on the panel due to e.g. a high zoom value will not have a visible label either. a filter for the peak labels (if supplied). Can be useful for highlighting only a subset of peaks with peak labels (e.g. only one data trace, or only those in a certain portion of the chromatogram). Only interpreted if peak_table is set. styling options to be used for the geom_label_repel peak labels. All parameters suppored by geom_label_repel are allowed. Particularly useful ones are size, force, nudge_x, nudge_y, segment.color ("black" is set by default, switch to NULL to get the same as the color aesthetic), segment.size and segment.alpha. deprecated - please use peak_label_options(size = 5) instead. deprecated - please use peak_label_options(force = 2) instead. a data frame of the chromatographic data prepared for plotting (see iso_prepare_continuous_flow_plot_data)

Other plot functions: iso_mark_calibration_range(), iso_mark_outliers(), iso_mark_value_range(), iso_mark_x_range(), iso_plot_data(), iso_plot_dual_inlet_data(), iso_plot_raw_data(), iso_plot_ref_peaks(), iso_plot_residuals(), iso_plot_scan_data(), iso_prepare_continuous_flow_plot_data(), iso_prepare_dual_inlet_plot_data(), iso_prepare_scan_plot_data()