In bihealth/metaquac: Metabolomics Targeted Quality Control

Calibration {.tabset}

Calibration scatter plots are reconstructed to enable an impression of calibration performance and range placement (in particular for 7-point calibrated compounds). To properly reflect the internal standard calibration method, areas and intensities are normalized by the ISTD areas and intensities, resp.

The following visualization is based on the status-preprocessed dataset 2b.

# Select dataset
biocrates <- datasets$filter_compounds_by_qc_rsd_kept

# Dynamic figure height
num_columns <- 7
num_compounds <- length(unique(biocrates$Compound))
compound_figure_height <- ceiling(num_compounds / num_columns) * 1 + 1

if (meas_type == "LC"){
  cat("\n### Concentration vs peak area\n")
  plot_compound_scatter(data = biocrates,
                        x = ENV$CONCENTRATION,
                        y = "Analyte Peak Area [area]",
                        y_istd = "Internal Std. Peak Area [area]",
                        sample_types = c(SAMPLE_TYPE_BIOLOGICAL,
                                         ENV$SAMPLE_TYPE_REFERENCE_QC,
                                         SAMPLE_TYPE_POOLED_QC,
                                         paste0("Standard L", 1:7)),
                        aspect = FALSE,
                        shape = BATCH,
                        ncol = num_columns)
}

Concentration vs intensity

plot_compound_scatter(data = biocrates,
                      x = ENV$CONCENTRATION,
                      y = "Analyte Intensity [cps]",
                      y_istd = "Internal Std. Intensity [cps]",
                      sample_types = c(SAMPLE_TYPE_BIOLOGICAL,
                                       ENV$SAMPLE_TYPE_REFERENCE_QC,
                                       SAMPLE_TYPE_POOLED_QC,
                                       paste0("Standard L", 1:7)),
                      aspect = FALSE,
                      shape = BATCH,
                      ncol = num_columns)

# Remove "biocrates" dataset to ensure following sections select the dataset they need
rm(biocrates)

bihealth/metaquac documentation built on Aug. 7, 2021, 8:40 a.m.