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library(ragg) knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 6, fig.height = 5, dev = "ragg_png" )
Load the spant package:
library(spant)
Load some example data for preprocessing:
fname <- system.file("extdata", "philips_spar_sdat_WS.SDAT", package = "spant") mrs_data <- read_mrs(fname, format = "spar_sdat")
Plot the spectral region between 4 and 0.5 ppm:
plot(mrs_data, xlim = c(4, 0.5))
Apply a 180 degree phase adjustment and plot:
mrs_data_p180 <- phase(mrs_data, 180) plot(mrs_data_p180, xlim = c(4, 0.5))
Apply 3 Hz Guassian line broadening:
mrs_data_lb <- lb(mrs_data, 3) plot(mrs_data_lb, xlim = c(4, 0.5))
Zero fill the data to twice the original length and plot:
mrs_data_zf <- zf(mrs_data, 2) plot(mrs_data_zf, xlim = c(4, 0.5))
Apply a HSVD filter to the residual water region and plot together with the original data:
mrs_data_filt <- hsvd_filt(mrs_data) stackplot(list(mrs_data, mrs_data_filt), xlim = c(5, 0.5), y_offset = 10, col = c("black", "red"), labels = c("original", "filtered"))
Apply a 0.1 ppm frequency shift and plot together with the original data:
mrs_data_shift <- shift(mrs_data, 0.1, "ppm") stackplot(list(mrs_data, mrs_data_shift), xlim = c(4, 0.5), y_offset = 10, col = c("black", "red"), labels = c("original", "shifted"))
Multiple processing commands may be conveniently combined with the pipe operator "|>" :
mrs_data_proc <- mrs_data |> hsvd_filt() |> lb(2) |> zf() plot(mrs_data_proc, xlim = c(5, 0.5))
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