NanoSIMS data processing of LANS data in R: HMR files • lans2r

library(lans2r)
library(dplyr)
library(knitr)
library(ggplot2)

This vignettes illustrates how to read and visualize data from HMR (=ion beam scan) files generated by the NanoSIMS software. These are primarily tuning files that are valuable for visualizing and evaluating how tuning parameters affect the peak shapes. This functionality is completely independent from LANS.

hmr <- load_HMR(system.file("extdata", "nanosims_data", "hmr", package = "lans2r"), 
                prefix = "", suffix = ".hmr_txt")

Settings overview

hmr %>% select(-step, -voltage, -cts) %>% distinct() %>% kable()

ion	prefix	filename	date	trolley	B	R	M
1H		/space/ims/data/Kopf/April_2014/PA_5e_1H.hmr	2014-02-04 21:32:00	#0	998.7	130.53	1.025
2H		/space/ims/data/Kopf/April_2014/PA_5e_2H.hmr	2014-02-04 21:32:00	#1	998.7	184.90	2.056

Scan overview

hmr %>% 
  ggplot() +
  aes(voltage, cts, color = ion) + 
  geom_line() +
  scale_y_log10("counts") +
  facet_wrap(~ion, scales = "free")