Embedded Files
Krona
Krona
Krona is a tool for visualizing the composition of our community.
The resulting file is an HTML file containing an interactive visualization. You can hover or click on any section of the Krona pie chart to get more details.
Question: What percentage of your sample was labelled Lactobacillus?
Explore the Krona plot, click on the Lactobacillus segment and the right-hand side will show you the percentages at any point in the hierarchy (here 5% of all Bacteria/Root).
Generating per-sample Krona plots (to visualize individual samples)
Generating per-sample Krona plots (to visualize individual samples)
You may have noticed that this plot shows the results for all samples together. In many cases however, you would like to be able to compare results for different samples.
In order to save computation time, mothur pools all reads into a single file, and uses the count table file to keep track of which samples the reads came from. However, Krona does not understand the mothur count table format, so we cannot use that to supply information about the groups. But luckily we can get Classify.otu to output per-sample taxonomy files. In the following exercise, we will create a Krona plot with per-sample subplots.
Remember to click and select the "folder" icon (marked with the pink rectangle) prior to selecting the file from the drop-down menu, for each of these two steps.
Assignment 2
Assignment 2
Once the "Per-Sample" Krona tree is completed, you have finished with the last assignment for the Galaxy Project. Check Canvas for the guidelines on how to prepare and submit assignment 2. You may choose to continue into the steps below and generate Phinch visualizations, but these activities are just for fun. They will not be covered in class.
Phinch
Phinch
We may now wish to further visualize our results. We can convert our shared file to the more widely used biom format and view it in a platform like Phinch.
download the generated BIOM file from Galaxy, rename the file extension from biom1 to biom, and upload it directly to the Phinch server at https://usegalaxy.eu/phinch/.
Click BROWSE to select the GalaxyXXXXX.biom file that you downloaded to from Galaxy and click LOAD FILE.
You should be able to see the SAMPLE NAME and the number of sequencing reads. Click PROCEED TO GALLERY
Click on any of the chart to plot your data. Let's try making a Taxonomy Bar Chart. You will see an interactive plot that looks like the following.
If you hover a particular bar within the plot, you will see the details about a sample.
You can try out other chart types to see how Phinch uses different ways to visualize the composition of the microbial community.
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