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Flow Injection

# load libraries
library(isoorbi) # for Orbitrap functions
library(dplyr) # for data wrangling
library(ggplot2) # for data visualization

Data

Load data

# load and process data
data <- 
  # load file included in isoorbi package
  system.file(package = "isoorbi", "extdata", "testfile_flow.isox") |>
  orbi_read_isox() |>
  orbi_simplify_isox() |>
  # define data block where signal is stable (plateau)
  orbi_define_block_for_flow_injection(start_time.min = 0.1, end_time.min = 0.9) |>
  # flag extreme TICxIT values
  orbi_flag_outliers(agc_fold_cutoff = 2)

Calculations

Ratios

# basepeak & ratios
data_w_basepeak <- 
  data |>
  orbi_define_basepeak("M0")

# ratio summaries
data_summary <- 
  data_w_basepeak |>
  orbi_summarize_results(ratio_method = "sum")

Figures

Visualize data

orbi_plot_raw_data(data, y = ions.incremental, y_scale = "log")

Ions of isotopocules in time

Raw ratios

data_w_basepeak |> orbi_plot_raw_data(y = ratio)

Isotopocule ratios vs M0

Ratios for 18O

fig <- 
  data_summary |>
  filter(isotopocule == "18O") |>
  # plot
  ggplot() +
  aes(
    x = filename,
    y = ratio, ymin = ratio - ratio_sem, ymax = ratio + ratio_sem,
    color = filename, shape = filename
  ) +
  geom_pointrange() +
  scale_color_brewer(palette = "Dark2") +
  # theme definitions
  theme_bw() +
  theme(
    text = element_text(size = 16),
    panel.grid = element_blank()
  ) +
  # labels
  labs(
    y = expression("ratio ("^18*O/M0*")")
  )
fig

Isotopocule ratios 18O vs M0

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.