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Tidy and Streamlined Metabolomics Data Workflows
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yasche/metamorphr
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The metamorphr package is intended to make working with metabolomicsdata more fun. For this, metamorphr introduces atidydata format which stores metabolomics data and associated metadata, aswell as MS/MS spectra in onetibble andincludes a set of functions to facilitate tasks typically encounteredduring metabolomics data analysis. This approach allows for an easyintegration withTidyverse packages,including ggplot2 and dplyr.
Install the stable version from CRAN with:
install.packages("metamorphr")Alternatively, you can install the development version of metamorphrfromGitHub with:
# install.packages("pak")pak::pak("yasche/metamorphr")
Here is an overview of currently implemented functions.
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()
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()
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Tidy and Streamlined Metabolomics Data Workflows
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