knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
Isoprocessor supports several plotting and data conversion functions for scan data. This vignette shows some of the functionality for scan files read by the isoreader package (see the corresponding vignette for details on data retrieval, storage and export).
# load isoreader and isoprocessor packages library(isoreader) library(isoprocessor)
# read scan examples provided by the isoreader package scan_files <- iso_read_scan( iso_get_reader_example("peak_shape_scan_example.scn"), iso_get_reader_example("background_scan_example.scn"), iso_get_reader_example("full_scan_example.scn"), iso_get_reader_example("time_scan_example.scn") )
Plotting the raw data can be done either with the generic iso_plot_raw_data()
function for a simple plot with default parameters, or directly using the scan specific iso_plot_scan_data()
:
iso_plot_scan_data(scan_files, type = "High Voltage")
iso_plot_scan_data(scan_files, type = "MagnetCurrent")
iso_plot_scan_data(scan_files, type = "Clock")
All customization options are described in the function help (?iso_plot_scan_data
) and include, for example, plotting only a specific subset of masses:
# plot just masses 44 and 45 iso_plot_scan_data( scan_files, type = "High Voltage", data = c("44", "45") )
Isoprocessor provides a dynamic ratio calculation function (iso_calculate_ratios()
) that accepts any combination of masses, here demonstrated for several different ratios. In this context, another useful customization option of the plotting function is the option to adjust plot aesthetics such as color, shape, and paneling:
scan_files <- scan_files %>% # calculate 46/44, 45/44 iso_calculate_ratios(ratios = c("46/44", "45/44")) iso_plot_scan_data( scan_files, type = "High Voltage", # visualize masses and ratios data = c(44:46, "45/44", "46/44"), # focus on peak x_interval = c(9.44, 9.49), # panel including by category panel = category ~ file_id )
Isoprocessor can convert between different signal units to examine the primary ion currents.
scan_files %>% # convert all signals to nano ampere iso_convert_signals(to = "pA") %>% # plot primary ion currents iso_plot_scan_data(data = c(44, 45))
Since all isoprocessor plots are standard ggplot objects, they can be modified with any ggplot commands.
library(ggplot2) # replot iso_plot_scan_data(scan_files, type = "MagnetCurrent") + # modify plot styling (ggplot functionality) theme(text = element_text(size = 20))
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