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:
VIEWpoly
interface containing the analysis complete
resultsWe 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:
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
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.
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.