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
Relative Abundance
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 .taxonomy file.
This is the unedited .taxonomy file that is an output to the
classify.otu
command in Mothur.
Click here to download an example file:
Download sample.taxonomy File
2. Upload your .shared file.
This is the unedited .shared file that is an output to the
make.shared
command in Mothur.
Click here to download an example file:
Download sample-abundance.shared File
3. 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 design.txt File
(3A.) First,
your design file must have a column of Sample ID names that
exactly
matches the Sample ID names found in your .shared file.
(3B.) Second,
the Sample ID column name must be
'Sample'.
(3C.) Third,
your design file must have a column that outlines the different experimental groups you wish to sort your data by.
(3D.) 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:
4. Navigate to the 'View Plots' tab, it may take over one minute to appear.
By default, the 'Phylum' level will be plotted.
5. Navigate to the 'Plots' tab to change which taxonomy level to plot.
6. Navigate to the 'Appearance' tab and make modifications.
Each modification will cause the plot to recalculate, please allow for one minute for the plot to appear.
7. Navigate to the 'Download' tab and download your plot in your preferred format.
Clicking download will cause the plot to calculate for a final time, so allow one minute for the image download to start. It is possible the download request will timeout if the data processing takes over one minute.
In that case
right click on the plot image in the 'View Plots' tab and you should be able to download the image that way.
Quick Overall Summary:
Relative Abundance Plots provide a visually pleasing way to look at microbiome data. See how different phyla of bacteria compare to one another within any given sample, as well as within any given group.
The phyla of bacteria are automatically selected from the .shared file you upload. The .shared file uses the .taxonomy file as a reference to get the taxonomy information of the OTUs that are in your .shared file. The .design file outlines meta data. Meta data could be which samples belong to which groups, the sex of the different samples, or the age of the different samples.