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Shiny interface for the Lipid Mining and Ontology (Lipid Mini-On) tool, which uses the Rodin R package

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PNNL-Comp-Mass-Spec/LipidMiniOn

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Lipid Mini-On

The Lipid Mining and Ontology (Lipid Mini-On) tool is a Shiny app that uses the Rodin R package. to create ontology bins and perform lipid enrichment analysis.

Running Lipid Mini-On

To use Lipid Mini-On, you need to run it as a local Shiny app; required steps:

install.packages(c("shiny", "plotly", "visNetwork", "shinycssloaders", "markdown"))
install.packages(c("ggplot2", "grid", "gridExtra", "gtable", "MASS", "plyr", "reshape2", "scales", "stats", "tibble", "lazyeval", "DT"))

install.packages("devtools")
devtools::install_github('https://github.com/PNNL-Comp-Mass-Spec/Rodin')

# Either load all of the libraries at once (using "invisible()" since the output from lapply() is not useful)
invisible(lapply(c("ggplot2", "grid", "gridExtra", "gtable", "MASS", "plyr", "reshape2", "scales", "stats", "tibble", "lazyeval", "DT"), library, character.only = TRUE))

# Or load each library individually
library(ggplot2)
library(grid)
library(gridExtra)
library(gtable)
library(MASS)
library(plyr)
library(reshape2)
library(scales)
library(stats)
library(tibble)
library(lazyeval)
library(DT)

# Load Shiny and required libraries
invisible(lapply(c("shiny", "plotly", "visNetwork", "shinycssloaders", "markdown"), library, character.only = TRUE))

# Start the Shiny app
runApp('C:/R/LipidMiniOn')

Lipid Mini-On will appear in a new window

Testing Lipid Mini-On

Directory C:\R\LipidMiniOn has several .csv files that can be used for testing

Steps to load process the data

  • Click Browse under "Upload 'Query' Lipid Names (.csv)"
    • Select file Soil_surface_signif.csv
  • Click Browse under "Upload 'Universe' Lipid Names (.csv)"
    • Select file Soil_universe.csv
  • Click "Check Data"
  • Click "Visualize" to see two stacked bar charts

Contacts

Written by Sarah Reehl and Kelly Stratton for the Department of Energy (PNNL, Richland, WA)
E-mail: geremy.clair@pnnl.gov or proteomics@pnnl.gov
Website: https://www.pnnl.gov/integrative-omics or https://panomics.pnnl.gov/

See the About.md file for more information about the developers

License

Lipid Mini-On is licensed under the 2-Clause BSD License; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2018 Battelle Memorial Institute

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Shiny interface for the Lipid Mining and Ontology (Lipid Mini-On) tool, which uses the Rodin R package

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