In tidymass/massqc: Quality assessment of LC-MS based metabolomics data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = TRUE,
  out.width = "100%"
)

Data preparation

library(massdataset)
library(tidyverse)
library(massqc)
data("sample_info", package = "massdataset")
data("expression_data", package = "massdataset")
data("variable_info", package = "massdataset")
object =
  create_mass_dataset(
    expression_data = expression_data,
    sample_info = sample_info,
    variable_info = variable_info
  )
object

Sample boxplot

 object %>%
   massqc_sample_boxplot()

 object %>%
   log(10) %>%
   massqc_sample_boxplot()

 object %>%
   log(10) %>%
   massqc_sample_boxplot(color_by = "class")

 object %>%
   log(10) %>%
   massqc_sample_boxplot(fill_by = "class") +
   ggsci::scale_fill_lancet()

 object %>%
   log(10) %>%
   massqc_sample_boxplot(
     fill_by = "class",
     color_by = "class",
     point = TRUE,
     point_alpha = 0.3
   ) +
   ggsci::scale_fill_lancet()

 object %>%
   log(10) %>%
   massqc_sample_boxplot(color_by = "class",
                  point = TRUE,
                  point_alpha = 0.3) +
   ggsci::scale_color_lancet()