filter top genera level heatmaps

User Support
1

Hi everyone!
I'm having some difficulties creating a heatmap. I created a collapsed table from the merged table at the genus level and I wanted to include the most abundant OTUs.

First of all, I tried to filter the collapsed-table to only include the top 10 genus. As I read in another topic (filtering features for top genera and exclusive features - #2 by ChrisKeefe), I checked the collapsed-table.qzv that I created and used the --p-min-frequency (with the frequency of the 10th most abundant feature, 1245).
But it fails, the filtered table that is created seems to be empty. So, may I be wrong choosing the frequency? Do I have to do it in a different way? I've tried it several times with different frequencies and I always got an empty table.

Captura
Captura1244Ă—485 59.7 KB

These are the commands that I used.
qiime feature-table filter-features
--i-table collapses-table.qza
--p-min-frequency 1500
--o-filtered-table filtered-table.qza
--m-metadata-file protozoos-metadata.tsv \

I also wanted to exclude the Unassigned features. Is it possible to do both things? I mean, if I know that the "Unassigned" is one of the top 10 features, should I choose the 11th most abundant frequency and exclude the unassigned?
Sorry if I'm mixing things up, but I'm a new user and I'm still learning how everything works. I'm a little bit confused. :sweat_smile: :sweat_smile:

One last thing I wanted to know is if it is possible to modify the x-axis of the heatmap. Instead of showing all the taxonomy of each OTU, would it be possible to show only the last taxonomy level assigned?
There is too much text and I would like to reduce it to the maximum level assigned.
Because, editing the axes is impossible with Qiime2, isn't it?
For example, writing for each feature the last assigned level as N_X (where X is the number of the taxonomy level), followed by the name of the assigned taxonomy. Is it possible?

I hope I have communicated my doubts well, thank you very much in advance. :blush:

2

Hi, @SaraGajas! :wave:

Let's see if we can figure out what's going on here, starting with your original question. Based on the screenshot and what you've told me, I'm not sure why you're getting an empty feature table. Here are a few questions:

  • :clown_face: Silly question: how did you conclude your feature table was empty?
  • are you able to share your collapsed table? (feel free to DM privately)

I'm curious if there's an issue with your command:

Firstly, I noticed a possible typo with –i-table collapses-table.qza (collapses instead of collapsed?). As always, make sure you are passing in the correct file names. Secondly, the last part of this command –m-metadata-file protozoos-metadata.tsv shouldn't be necessary at this point. I would leave that off for this particular filtering step. Lastly, the trailing \ at the end of the command is a bit suspect. It shouldn't cause any problems, but it's another small bit of evidence that your observations might be the result of a typo.

Lastly, I believe this section of the filtering tutorial should answer your other filtering question:

3

Because after filtering the table, and creating the heatmap, a message saying "plugin error from feature-table: cannot visualize an empty table" appeared.

Sorry, it's just that transcribing here the commands I used I made a mistake. :sweat_smile:

The same here :sweat_smile:

IT WORKED!! I've filtered the collapsed-table again without using the metadata-file and the heatmap was created as expected. :star_struck: :star_struck:

About this, I will have a look to see if I can get it.

Thank you very much!!!!! :qiime2: