Dataset QA summary

In spant: MR Spectroscopy Analysis Tools

library(spant)
library(ggplot2)
knitr::opts_chunk$set(echo = FALSE)
theme_set(theme_bw())
n_spec <- length(params$data$summary$labels)
spec_fig_h <- max(c(5, n_spec * 0.4))
bar_fig_h  <- max(c(4, n_spec * 0.2))

Spectra

Dynamic mean

plot_labs <- params$data$summary$labels[rev(1:length(params$data$summary$labels))]
proc_list <- params$data$res_list |> lapply(\(x) x$mean_corr)
proc_list <- proc_list[rev(1:length(proc_list))]
proc_list |> zf() |> stackplot(xlim = c(4, 0.5), y_offset = 50,
                               labels = plot_labs,
                               mar = c(3.5, 1, 1, 6), bl_lty = 2,
                               yaxs = "i")

First dynamic

proc_list <- params$data$res_list |> lapply(\(x) x$corrected)
proc_list <- proc_list[rev(1:length(proc_list))]
proc_list |> get_dyns(1) |> zf() |> stackplot(xlim = c(4, 0.5), y_offset = 50,
                                    labels = plot_labs,
                                    mar = c(3.5, 1, 1, 6), bl_lty = 2,
                                    yaxs = "i")

Last dynamic

proc_list <- params$data$res_list |> lapply(\(x) x$corrected)
proc_list <- proc_list[rev(1:length(proc_list))]
last_dyn  <- proc_list[[1]] |> Ndyns()
proc_list |> get_dyns(last_dyn) |> zf() |> stackplot(xlim = c(4, 0.5),
                                           y_offset = 50,
                                           labels = plot_labs,
                                           mar = c(3.5, 1, 1, 6), bl_lty = 2,
                                           yaxs = "i")

Summary metrics

Dynamic mean corrected spectral linewidths

ggplot(params$data$summary, aes(x = mean_corr_spec_lw, y = labels)) +
  geom_col() + ylab("") + xlab("Linewidth for mean corrected data (ppm)") +
  scale_y_discrete(limits = rev)

Median single shot SNR

ggplot(params$data$summary, aes(x = ss_median_spec_snr, y = labels)) + 
  geom_col() + ylab("") + xlab("Median single shot SNR") +
  scale_y_discrete(limits = rev)

Dynamic frequency shifts range

ggplot(params$data$summary, aes(x = shift_hz_range, y = labels)) + geom_col() + 
      ylab("") + xlab("Shift range (Hz)") + scale_y_discrete(limits = rev)

Smoothed dynamic linewidths range

ggplot(params$data$summary, aes(x = lw_ppm_smo_range, y = labels)) + 
  geom_col() + ylab("") + xlab("Smoothed linewidth range (ppm)") +
  scale_y_discrete(limits = rev)

Dynamic lipid fluctuation range

ggplot(params$data$summary, aes(x = dlfr * 100, y = labels)) +
  geom_col() + ylab("") + 
  xlab("Dynamic lipid fluctuation range (% tCr intensity)") +
  scale_y_discrete(limits = rev)

Dynamic fluctuation range

ggplot(params$data$summary, aes(x = dfr * 100, y = labels)) +
  geom_col() + ylab("") + xlab("Dynamic fluctuation range (% tCr intensity)") +
  scale_y_discrete(limits = rev)

Dataset quality summary

Dataset mean single shot SNR : r round(mean(params$data$summary$ss_median_spec_snr), 1)

Dataset standard deviation single shot SNR : r round(sd(params$data$summary$ss_median_spec_snr), 1)

Dataset mean spectral linewidth : r round(mean(params$data$summary$mean_corr_spec_lw), 3)

Dataset standard deviation spectral linewidth : r round(sd(params$data$summary$mean_corr_spec_lw), 3)

if (!is.null(params$data$exclude_labels)) {
  cat("### Excluded scan labels\n")
  for (x in params$data$exclude_labels) cat("- ", x, "\n")
}

spant documentation built on Dec. 16, 2025, 5:09 p.m.