Creation of Diversity tutorial #4282

Sophia120199 · 2023-07-13T17:59:48Z

Hi, so this is the draft of a tutorial on how to calculate alpha and beta diversity, I'm looking forward to the review feedback :)

There are still some unsolved issues:

I didn't understand how to interpret the results of the fisher's alpha index calculated by krakentools, so the explanation for this is still missing
the zenodo files with the bracken output as starter input files for the tutorial still need to be created
somehow in the detail box on renyie entropy, the mathematical expression is already visible, when the box is not opened yet, I don't know why
in the preview website, the mathematical expressions of the alpha diversity are not shown correctly since I added the $$ signs

paulzierep

Small text adjustments and some suggestions for better explanation of krakentools alpha diversity

topics/metagenomics/tutorials/diversity/tutorial.md

paulzierep · 2023-07-19T10:45:32Z

topics/metagenomics/tutorials/diversity/tutorial.md

+
+   S is number of taxa, n is number of individuals and a is the Fisher's alpha.                                                                                                                                                                     
+
+**KrakenTools** is a suite of scripts designed to help Kraken users with downstream analysis of Kraken results. The Krakentool **Calculate alpha diversity** offers the possibility to calculate five different alpha diversity indexes:


The output of bracken consists of all taxonomic levels: K_kingdom, P_phylum, C_class, O_order, F_family, G_genus, and S_species ; hence the alpha diversity is also calculated using all that levels. In think in most cases, alpha diversity is defined as "generally based on the number and relative abundance of taxa at some rank" ...maybe that could be explained as well.
Technically, one could add a filter step before krakentools to achieve that.

It could be added as a detail box for people that uses Kraken output directly and not Braken one

yes a detail box sounds good, still what I said applies for Kraken and Braken

paulzierep · 2023-07-19T10:49:30Z

topics/metagenomics/tutorials/diversity/tutorial.md

+4. Inverse Simpson's diversity
+5. Fisher's index
+
+> <hands-on-title>Calculate α diversity with Krakentools</hands-on-title>


One could actually use Calculate α diversity with Krakentools for any tool that outputs taxonomy abundances, provided one converts it into the correct table format i.e. assigning column 5 as the abundance, in fact that would for any population data, maybe that could be addressed, since it would allow the usage in a more generic setting.

bebatut

Thanks a lot @Sophia120199. I made some suggestions of changes and also added some comments. We can talk about them tomorrow in our meeting

topics/metagenomics/tutorials/diversity/tutorial.md

bebatut · 2023-07-19T11:57:46Z

topics/metagenomics/tutorials/diversity/tutorial.md

+> Instead of selecting a few measures to describe an assemblage, it is preferable to **present a continuous profile** that depicts diversity or entropy as a function of q (where q ≥ 0). This approach enables a visual comparison of the compositional complexities among multiple assemblages and facilitates the assessment of the evenness in the relative abundance distributions of the assemblages. In practice, the profile is typically plotted for values of q ranging from 0 to q = 3 or 4, beyond which there is usually little change.
+>
+> ![Parameter q](./images/hill_numbers.png)
+> https://www.redalyc.org/journal/5117/511766773011/html/


What is this link? What does it refer to?

thats the source of the image

Maybe good to put as a caption then (in parenthesis after the path to the image)

bebatut · 2023-07-19T11:58:46Z

topics/metagenomics/tutorials/diversity/tutorial.md

+{: .details}
+
+
+> <details-title>More details on the Hill numbers</details-title>


Should that go with the Multidimensional metrics?

bebatut · 2023-07-19T11:59:02Z

topics/metagenomics/tutorials/diversity/tutorial.md

+{: .details}
+
+
+> <details-title>More details on the Rényi entropy</details-title> 


Should that go with the Multidimensional metrics?

bebatut · 2023-07-19T11:59:32Z

topics/metagenomics/tutorials/diversity/workflow/test

@@ -0,0 +1 @@
+


Can you add the workflow there? And tests? Thanks

Co-authored-by: Bérénice Batut <[email protected]> Co-authored-by: paulzierep <[email protected]>

paulzierep

comment for Calculate beta diversity

paulzierep · 2023-08-22T14:43:30Z

topics/metagenomics/tutorials/diversity/tutorial.md

+> Some of the key features and functionalities of QIIME 2 include:
+> 1. Data Import and Preprocessing: QIIME 2 supports the import of raw sequencing data and performs quality control and data preprocessing steps, such as demultiplexing, quality filtering, and primer removal.
+> 2. Taxonomic Assignments: The software enables taxonomic classification of microbial sequences using various algorithms and reference databases.
+> 3. Diversity Analysis: QIIME 2 allows users to explore and quantify microbial diversity within and between samples. It provides metrics for alpha diversity (within-sample diversity) and beta diversity (between-sample diversity).
+> 4. Community Analysis: Users can investigate the composition and structure of microbial communities, including taxonomic summaries, abundance profiles, and statistical comparisons between groups.
+> 5. Phylogenetic Analysis: QIIME 2 supports the construction of phylogenetic trees to infer evolutionary relationships among microbial taxa and perform phylogenetic diversity analysis.
+> 6. Statistical Analysis: The software offers a wide range of statistical methods for differential abundance analysis, correlation analysis, multivariate analysis, and other types of statistical tests.
+> 7. Visualization: QIIME 2 provides interactive and customizable visualizations to aid in the exploration and interpretation of microbiome data, including heatmaps, bar plots, PCoA plots, and taxonomic trees.


I agree, I think the most important information would be to state, that Calculate beta diversity with quiime has much more metric, but requires a different input format.

shiltemann · 2024-01-15T21:14:42Z

Hi @Sophia120199! Thanks a lot for your tutorial! Just wanted to let you know that we renamed the metagenomics topic to "microbiome", so I have also changed this in your PR. So please update your local branch to pull in these changes before adding more edits :)

bebatut · 2024-01-16T08:16:30Z

@Sophia120199 is not working with us anymore
@paulzierep could you have a look at this PR and see if more changes are needed to merge it? Thanks a lot

paulzierep · 2024-02-13T09:58:41Z

sorry I missed that completely, will try to review in the next days ...

paulzierep · 2024-04-22T09:29:46Z

Still need to review this, will try my best !

paulzierep

do we know where the test files are ?

paulzierep · 2024-04-22T09:32:56Z

topics/microbiome/tutorials/diversity/tutorial.md

+---
+layout: tutorial_hands_on
+title: Calculating α and β diversity from microbiome taxonomic data
+zenodo_link: xxx


I guess we need some test data and a workflow for this.

topics/microbiome/tutorials/diversity/tutorial.md

paulzierep · 2024-08-01T10:43:34Z

topics/microbiome/tutorials/diversity/tutorial.md

@@ -0,0 +1,437 @@
+---
+layout: tutorial_hands_on


Suggested change

layout: tutorial_hands_on

layout: tutorial_hands_on

draft: true

Do you want to have it as a draft tutorial?

until I fix it yes

never mind, I merged too early, lets fix it now

shiltemann · 2024-08-01T11:11:51Z

@paulzierep looks like you merged this while the build test was failing, so this (and any future updates to GTN) will not go live until that is addressed, do you have time to have a look at the faillure or should I?

shiltemann · 2024-08-01T11:22:49Z

(I'm on it)

paulzierep · 2024-08-01T11:24:25Z

Yes, sorry,, will fix it here: #5191

shiltemann · 2024-08-01T11:28:01Z

all good, I pushed a fix directly to main, just waiting to see if it builds now

paulzierep · 2024-08-01T11:45:08Z

thanks @shiltemann ; I am fixing the rest here atm

Sophia120199 added 28 commits June 29, 2023 14:02

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Sophia120199 requested a review from a team as a code owner July 13, 2023 17:59

github-actions bot added the metagenomics label Jul 13, 2023

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Sophia120199 and others added 4 commits July 20, 2023 11:06

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Co-authored-by: Bérénice Batut <[email protected]> Co-authored-by: paulzierep <[email protected]>

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Creation of Diversity tutorial #4282

Creation of Diversity tutorial #4282

Sophia120199 commented Jul 13, 2023

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		S is number of taxa, n is number of individuals and a is the Fisher's alpha.

		KrakenTools is a suite of scripts designed to help Kraken users with downstream analysis of Kraken results. The Krakentool Calculate alpha diversity offers the possibility to calculate five different alpha diversity indexes:

		{: .details}


		> <details-title>More details on the Hill numbers</details-title>

		{: .details}


		> <details-title>More details on the Rényi entropy</details-title>

	layout: tutorial_hands_on
	layout: tutorial_hands_on
	draft: true

Creation of Diversity tutorial #4282

Creation of Diversity tutorial #4282

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Sophia120199 commented Jul 13, 2023

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shiltemann commented Aug 1, 2024 • edited Loading

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