VIEWpoly is also a useful tool to make complete results of different analyses available. You may want to do this for different reasons. For example:

  • Provide a link in your paper to direct readers to a VIEWpoly interface containing the analysis complete results
  • Store in your lab computer the results from different analyses so other lab members can easily consult it

We created a specific version of VIEWpoly that can display your datasets without the need to upload the files. Your datasets will be automatically displayed the same way our potato example data is in the main version. For this, you will need to create your own version of VIEWpoly. We will guide you on how to do it in three simple steps:

Download VIEWpoly version for publishing data

The modified VIEWpoly version is in the branch publishing_data. First, go to VIEWpoly publishing_data branch github page:

Click in Code and then Download ZIP:

Once the ZIP file is downloaded, decompress it in a chosen location.

Instead of downloading the ZIP you can clone the VIEWpoly version to your computer using:

git clone -b publishing_data https://github.com/mmollina/viewpoly.git

Add your data

In the viewpoly downloaded directory you will find an R package common structure. This contains all code required to run VIEWpoly. You will include your viewpoly objects in the directory viewpoly/inst/ext/my_viewpoly_objects/. If your genomic information is contained in local files instead of links (see more about genomic input data in the main VIEWpoly tutorial) you should include them in the viewpoly/inst/ext/my_genomes/ directory.

After, you should edit the file viewpoly/inst/ext/info_data.csv. This file is used to identify and connect the viewpoly objects with the genomic information. Each row contains information on one dataset. Observe that you can combine different viewpoly objects with different genome information, it is important to remember to set a unique ID by row. Complete with NULL if you don’t have some of the genomic information.

Run

  • Locally

To check if the changes worked, open the file app.R located at viewpoly/app.R and click on the Run app button in the right superior corner of your script window in RStudio.

If you want to run the app using only run_app() command you need to install the package with your modifications. An easy way of doing this in RStudio is to create a project (superior corner of the Rstudio window) by selecting the viewpoly directory.