The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

Maintenance: Tues, 28 Jan 2020


Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
User Portal                   8:00am to 5:00pm MST
The User Portal,, will be unavailable while we perform maintenance and updates.
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA

Keep up to date with our maintenance schedules on the CyVerse public calendar
Check your local timezone here 
Please contact for any questions, or concerns.






Skip to end of metadata
Go to start of metadata

Principal Component Analysis

Community rating: ?????

Performs Principal Component Analysis on Phenotypes. The script generates 5 files: pca_summary.txt by which we get information on the importance of components. The first row denotes the components that the data were analyzed, second row denotes the standard deviation third row the Proportion of Variance and the last one the Cumulative Proportion , pca_scores.txt assigns a score of each of the component to each of the samples, loadings.txt which describes the variation each of the factors,e.g. markers e.g. phenotype, contributes to each of the components, pca.pdf graphically represents the the contribution of each of the components and Rplots.pdf actually contains two graphs the first one represents graphically the outcome of pca_scores and the second includes also the direction of each of the loadings.. 

Quick Start

  • To use Principal Component Analysis, import your data in cvs format. The first row is the names of the markers or Phenotypes. The first column is the names of the samples and all the rest Phenotypes or markers
  • Resources: DE

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under _Community Data -> iplantcollaborative -> example_data ->_PCA.

Input File(s)

Use example_datamod.csv from the directory above as test input.

Output File(s)

Expect as output 5 files named pca_summary.txt, pca_scores.txt, loadings.txt, pca.pdf and Rplots.pdf . For the test case, the output files you will find in the example_data called PCA

  • No labels