1 Using DIMet in the command line

1.1 Using DIMet

DIMet runs in the command line environment.

1.1.1 Using DIMet with provided datasets

To test the use of DIMet, we provide datasets, configuration and bash scripts corresponding to the results presented in the manuscript "DIMet: An open-source tool for Differential analysis of Isotope-labeled targeted Metabolomics data" by J. Galvis et al. are available at Zenodo (manuscript_data):

• Download and uncompress the file datasets_manuscript_DIMet.zip.

  Whole structure of the downloaded folder _{^{(click to show/hide)}}

  datasets_manuscript_DIMet
  ├── config
  │   ├── analysis
  │   │   ├── abundance_plot_Cycloserine.yaml
  │   │   ├── abundance_plot_LDHAB-Control.yaml
  │   │   ├── dataset
  │   │   │   ├── Cycloserine_data.yaml
  │   │   │   ├── LDHAB-Control_data_integrate.yaml
  │   │   │   └── LDHAB-Control_data.yaml
  │   │   ├── differential_analysis_pairwise_LDHAB-Control.yaml
  │   │   ├── enrichment_lineplot_Cycloserine.yaml
  │   │   ├── isotopologues_plot_Cycloserine.yaml
  │   │   ├── isotopologues_plot_LDHAB-Control.yaml
  │   │   ├── metabologram_abundance_LDHAB-Control.yaml
  │   │   ├── metabologram_enrichment_LDHAB-Control.yaml
  │   │   ├── pca_plot_LDHAB-Control.yaml
  │   │   ├── pca_tables_Cycloserine.yaml
  │   │   └── timecourse_analysis_Cycloserine.yaml
  │   ├── general_config_abundance_plot_Cycloserine.yaml
  │   ├── general_config_abundance_plot_LDHAB-Control.yaml
  │   ├── general_config_differential_analysis_LDHAB-Control.yaml
  │   ├── general_config_enrichment_lineplot_Cycloserine.yaml
  │   ├── general_config_isotopologues_plot_Cycloserine.yaml
  │   ├── general_config_isotopologues_plot_LDHAB-Control.yaml
  │   ├── general_config_metabologram_abundance_LDHAB-Control.yaml
  │   ├── general_config_metabologram_enrichment_LDHAB-Control.yaml
  │   ├── general_config_pca_plot_LDHAB-Control.yaml
  │   ├── general_config_pca_tables_Cycloserine.yaml
  │   └── general_config_timecourse_analysis_Cycloserine.yaml
  ├── data
  │   ├── Cycloserine_data
  │   │   ├── CorrectedIsotopologues.csv
  │   │   ├── FracContribution_C.csv
  │   │   ├── metadata_cycloser.csv
  │   │   └── rawAbundances.csv
  │   └── LDHAB-Control_data
  │       ├── DEG_Control_LDHAB.csv
  │       ├── pathways_kegg_metabolites.csv
  │       ├── pathways_kegg_transcripts.csv
  │       ├── AbundanceCorrected.csv
  │       ├── IsotopologuesAbs.csv
  │       ├── IsotopologuesProp.csv
  │       ├── MeanEnrichment13C.csv
  │       └── metadata_endo_ldh.csv
  ├── run_Cycloserine_timeseries.sh
  └── run_LDHAB-Control.sh
  

• Make sure you have activated your virtual environment. In the datasets_manuscript_DIMet folder you have two .sh files: run_LDHAB-Control.sh and run_Cycloserine_timeseries.sh; Make them executable:

  chmod a+x *.sh
  

• and finally run:

  ./run_LDHAB-Control.sh
  ./run_Cycloserine_timeseries.sh
  

For more examples please download Zenodo (minimal_examples_DIMet_command_line)

1.1.2 Available analyses

• pca_analysis computes the PCA and outputs tables with principal components and explained variances
• pca_plot generates classical PCA plots
• abundance_plot plots with bars of total metabolite abundances
• mean_enrichment_line_plot generates lineplots of mean enrichment
• isotopologue_proportions_plot generates stacked bars of isotopologue proportions
• differential_analysis runs differential analysis and computes the corresponding statistics
• multi_group_comparison same as differential analysis before, but for > 2 groups
• time_course_analysis runs differential analysis for time-course experiments in pairwise fashion for consecutive time points
• bivariate_analysis runs the correlation test to compare MDV (Mass isotopomer Distribution Vector) profiles, and/or metabolite time-course profiles
• metabologram_integration pathway-based integration between labeled targeted metabolomic and trascriptomic data, resulting in metabologram plots

All these analyses can be executed using a generic command, their specifics are defined in the configuration file.

python -m dimet -cd config -cn GENERAL_CONFIGURATION_FILENAME

The -cd parameter must be set invariably as config (the directory containing the config files). The -cn parameter indicates the general configuration file name.

The command must be run from the parent directory of the config folder (see the clickable bullet 'Whole structure of the downloaded folder' in 1.1.1 Using DIMet with provided datasets).

The following sections of this Wiki page will guide you to compose your own analysis with the data and the configuration files required for running DIMet in the command line. We encourage the user to download the examples that we provide (Zenodo links in subsection 1.1.1), as they illustrate all the types of analyses. Go to 1.2 Organising your data for the analysis to start.