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metamorphr

The metamorphr package is intended to make working with metabolomics data more fun. For this, metamorphr introduces a tidy data format which stores metabolomics data and associated metadata, as well as MS/MS spectra in one tibble and includes a set of functions to facilitate tasks typically encountered during metabolomics data analysis. This approach allows for an easy integration with Tidyverse packages, including ggplot2 and dplyr.

💾 Installation

Install the stable version from CRAN with:

install.packages("metamorphr")

Alternatively, you can install the development version of metamorphr from GitHub with:

# install.packages("pak")
pak::pak("yasche/metamorphr")

⚙️ Functions

Here is an overview of currently implemented functions.

📑 Examples

✨ Create your analysis workflows in no time

library(metamorphr)
library(ggplot2)

toy_metaboscape %>%
  join_metadata(toy_metaboscape_metadata) %>%
  filter_blank(blank_samples = "blank",
               blank_as_group = T,
               group_column = Group) %>%
  filter_grouped_mv(min_found = 0.75) %>%
  impute_lod() %>%
  normalize_pqn() %>%
  scale_auto() %>%
  plot_pca(group_column = Group) +
    ggplot2::theme_bw()

📊 Seamlessly work with your data sets with dplyr and ggplot2

Easily plot the distribution of all intensities across samples

library(dplyr)

toy_metaboscape %>%
  join_metadata(toy_metaboscape_metadata) %>%
  ggplot2::ggplot(ggplot2::aes(Sample, Intensity, color = Group)) +
    ggplot2::geom_boxplot() +
    ggplot2::theme_bw()

… or compare the intensity of specific features across groups

toy_metaboscape %>%
  join_metadata(toy_metaboscape_metadata) %>%
  dplyr::filter(Name %in% c("Arachidonic acid", "ADP", "NADPH")) %>%
  dplyr::filter(Group %in% c("control", "treatment")) %>%
  ggplot2::ggplot(ggplot2::aes(Group, Intensity, color = Group)) +
    ggplot2::geom_boxplot() +
    ggplot2::facet_wrap(~Name) +
    ggplot2::theme_bw()

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.