Plot chromatogram from continuous flow data

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
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.
panel	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.
color	whether to color plot by anything, options are the same as for `panel` but the default is `file_id`
linetype	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`.
label	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`.
peak_table	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`.
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.
peak_marker	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.
peak_bounds	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.
peak_bgrd	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.
peak_label	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.
peak_label_filter	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.
peak_label_options	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`.
peak_label_size	deprecated - please use `peak_label_options(size = 5)` instead.
peak_label_repel	deprecated - please use `peak_label_options(force = 2)` instead.
df	a data frame of the chromatographic data prepared for plotting (see `iso_prepare_continuous_flow_plot_data`)

Arguments

See also