Description Usage Arguments See Also
View source: R/visualization.R
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
).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | iso_plot_continuous_flow_data(...)
## S3 method for class '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 class '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
)
|
... |
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. |
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 |
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 ( |
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 |
panel |
whether to panel plot by anything - any column or complex expression is possible (see notes in the |
color |
whether to color plot by anything, options are the same as for |
linetype |
whether to differentiate by linetype, options are the same as for |
label |
this is primarily of use for turning the generated ggplots into interactive plots via |
peak_table |
a data frame that describes the peaks in this chromatogram. By default, the peak table from the |
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 ( |
rt |
the column in the |
rt_start |
the column in the |
rt_end |
the column in the |
rt_unit |
which time unit the retention time columns ( |
peak_marker |
whether to mark identified peaks with a vertical line at the peak retention time. Only works if a |
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_bgrd |
NOT YET IMPLEMENTED whether to show the background of identified peaks from start to end retention times. Only works if a |
peak_label |
whether to label identified peaks. Any valid column or complex expression is supported and ALL columns in the provided |
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_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 |
peak_label_size |
deprecated - please use |
peak_label_repel |
deprecated - please use |
df |
a data frame of the chromatographic data prepared for plotting (see |
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()
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