A
Shiny app
allows you to visualize data by using R scripts without having to interact with the R script itself. This Shiny app will allow you to plot your
Alpha Diversity
microbiome data in an easy-to-view format. If this is your first time utilizing this Shiny app, follow the step below to start visualising your data now!
1. Navigate to the 'Inputs' tab and upload your .summary file.
This is the unedited .summary file that is an output to the
summary.single
command in Mothur.
Click here to download an example file:
Download sample.groups.summary File
2. Upload your design.txt file.
This is a .txt file that you must make on your own. This Shiny app has a few rules for formatting your design.txt file.
Click here to download an example file:
Download sample.alpha.design.txt File
(2A.) First,
your design file must have a column of Sample ID names that
exactly
matches the Sample ID names found in your .summary file. You'll find the Sample ID names under the
'groups'
column of your .summary file.
(2B.) Second,
the Sample ID column name must be
'Sample'.
(2C.) Third,
your design file must have a column that outlines the different experimental groups you wish to sort your data by.
(2D.) Fourth,
the group column mentioned in the third requirement must have the column name
'Group'.
An example of a compatible design.txt file is below:
3. Navigate to the 'Plot' tab and select your preferred Alpha Diversity metric.
4. Navigate to the 'Appearance' and the 'View Plots' tab and make modifications.
5. Navigate to the 'Download' tab and download your plot in your preferred format.