In jaspershen/massstat: Statistical analysis for 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(massstat)

data("liver_aging_pos")
liver_aging_pos

w_78 =
  liver_aging_pos %>%
  activate_mass_dataset(what = "sample_info") %>%
  dplyr::filter(group == "78W") %>%
  dplyr::pull(sample_id)

w_24 =
  liver_aging_pos %>%
  activate_mass_dataset(what = "sample_info") %>%
  dplyr::filter(group == "24W") %>%
  dplyr::pull(sample_id)

control_sample_id = w_24
case_sample_id = w_78

liver_aging_pos =
  mutate_fc(
    object = liver_aging_pos,
    control_sample_id = control_sample_id,
    case_sample_id = case_sample_id,
    mean_median = "mean"
  )

liver_aging_pos =
  mutate_p_value(
    object = liver_aging_pos,
    control_sample_id = control_sample_id,
    case_sample_id = case_sample_id,
    method = "t.test",
    p_adjust_methods = "BH"
  )

object = liver_aging_pos

Volcano plot

volcano_plot(
  object = object,
  fc_column_name = "fc",
  p_value_column_name = "p_value_adjust",
  labs_x = "log2(Fold change)",
  labs_y = "-log(p-adjust, 10)",
  fc_up_cutoff = 2,
  fc_down_cutoff = 0.5,
  p_value_cutoff = 0.05,
  add_text = TRUE
)


volcano_plot(
  object = object,
  fc_column_name = "fc",
  p_value_column_name = "p_value",
  labs_x = "log2(Fold change)",
  labs_y = "-log(p-value, 10)",
  fc_up_cutoff = 2,
  fc_down_cutoff = 0.5,
  p_value_cutoff = 0.05,
  add_text = FALSE,
  point_alpha = 0.5
)

volcano_plot(
  object = object,
  fc_column_name = "fc",
  p_value_column_name = "p_value",
  labs_x = "log2(Fold change)",
  labs_y = "-log(p-value, 10)",
  fc_up_cutoff = 2,
  fc_down_cutoff = 0.5,
  p_value_cutoff = 0.05,
  add_text = FALSE,
  point_alpha = 0.5,
  point_size_scale = "p_value"
) +
  scale_size_continuous(range = c(0.5, 3))