In dgiguer/omicplotR_pkg: Visual Exploration of Omic Datasets Using a Shiny App

Welcome to omicplotR!

omicplotR is a data visualization tool based on the Shiny framework to easily explore your multivariate 'omic' data.

Features

• Clustering using PCA biplots
• Filtering count tables by counts (per sample or OTU/gene)
• Filter data using metadata
• Colouring biplots using metadata
• Dendrograms and stacked barplots for taxonomic information
• Interactive effect plots using ALDEx2

Data format requirements

Data

1. The data file must be a tab delimited .txt (this is an option when you click 'Save as' from Excel).
2. The first column must contain gene/OTU identifier.
3. The first row must contain sample identifiers.
4. The last column may contain taxonomic level information, but is not required. If present, it must be labelled 'taxonomy'.
5. Data table must have all blank rows removed (this may require you to check in a text editor like Notepad ++ or Atom before using the app)

Metadata

1. Must be a tab delimited .txt (this is an option when you click 'Save as' from Excel).
2. The first column must contain sample identifiers. The sample identifiers must be identical to the data file (not required to be in the same order).
3. The first row must contain phenotypic information.

Saving Plots

To save your image, right-click the desired image and click 'Save picture as'.

dgiguer/omicplotR_pkg documentation built on Nov. 18, 2019, 6:31 p.m.