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# load libraries
library(isoorbi) # for Orbitrap functions
library(dplyr) # for data wrangling
library(ggplot2) # for data visualization
# 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)
[32m✔[39m [38;5;249m[231ms][39m [1morbi_read_isox()[22m loaded 6449 peaks for 1 compound ([32mHSO4-[39m) with 5
isotopocules ([32mM0[39m, [32m33S[39m, [32m17O[39m, [32m34S[39m, and [32m18O[39m) from [34mtestfile_flow.isox[39m
[32m✔[39m [38;5;249m[2ms][39m [1morbi_simplify_isox()[22m kept columns [32mfilepath[39m, [32mfilename[39m, [32mscan.no[39m,
[32mtime.min[39m, [32mcompound[39m, [32misotopocule[39m, [32mions.incremental[39m, [32mtic[39m, and [32mit.ms[39m
[32m✔[39m [38;5;249m[12ms][39m [1morbi_define_block_for_flow_injection()[22m added a new block (0.1 to 0.9
min) to 3 files
[32m✔[39m [38;5;249m[8ms][39m [1morbi_flag_outliers()[22m confirmed that none of the 1290 scans are [33moutliers[39m
based on [32m2 fold AGC cutoff[39m, i.e. based on [3mscans below 1/2 and above 2 times the[23m
[3maverage number of ions [32mtic[39m * [32mit.ms[39m in the Orbitrap analyzer[23m, in 6 data groups
(based on [32mfilename[39m, [32mblock[39m, and [32msegment[39m)
[32m✔[39m [38;5;249m[51ms][39m [1morbi_define_basepeak()[22m set [32mM0[39m as the ratio denominator and calculated
5.16k [32mratio[39m values for 4 isotopocules ([32m33S[39m, [32m17O[39m, [32m34S[39m, and [32m18O[39m)
[32m✔[39m [38;5;249m[26ms][39m [1morbi_summarize_results()[22m summarized ratios from 4.14k peak ([3mexcluding[23m
0 flagged peaks; [3mexcluding[23m 1.02k unused peaks) using the [1m[3msum[23m[22m method and
grouping the data by [32mfilename[39m, [32mcompound[39m, [32mbasepeak[39m, [32misotopocule[39m, [32mblock[39m,
[32msample_name[39m, [32msegment[39m, [32mdata_group[39m, and [32mdata_type[39m
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
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