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Tutorial Extension

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danielm710 edited this page Nov 19, 2020 · 16 revisions

Input preparation

Prior to following this tutorial, please download input files here

You should have following files:

  1. PCoA files (weighted/unweighted UniFrac, Bray-Curtis, Jaccard) (.qza)
  2. Feature table (labelled as merged_table.qza)
  3. Taxonomic classification result (labelled as taxonomy.qza)
  4. Metadata file (.tsv)
  5. Environmental metadata file (.tsv)

Custom PCoA plot

PCoA is used to project samples into multidimensional space while maximally preserving the original dissimilarity relationship between the samples.

While QIIME2 offers a way to visusalize ordination via emperor plot, you may use AXIOME3 to generate more customizable PCoA plot.

Input(s)

  1. QIIME2 archived PCoA artifact (.qza) (output from "Analysis" module) AXIOME3 generates four different types of PCoA ordinations,

    1. Unweighted UniFrac (named as 'unweighted_unifrac_pcoa.qza'). You may use sample Unweighted UniFrac PCoA (click here to download)
    2. Weighted UniFrac (named as 'weighted_unifrac_pcoa.qza'). You may use sample Weighted UniFrac PCoA (click here to download)
    3. Bray-Curtis (named as 'bray_curtis_pcoa.qza'). You may use sample Bray-Curtis PCoA (click here to download)
    4. Jaccard (named as 'jaccard_pcoa.qza'). You may use sample Jaccard PCoA (click here to download)

  2. Metadata file

    • It will be used to overlay metadata groups on triplot ordination. You may use sample metadata (click here to download)

Steps

For the tutorial, we will be using bray_curtis_pcoa.qza that was generated in the Analysis module, and metadata.tsv.

  1. Upload input files pcoa input

  2. Choose options pcoa step

  3. Start analysis

When it's done running it should look like the following

pcoa plot

  • Feel free to use other PCoA ordinations that are generated from different dissmilarity metrics.

  • Feel free to explore other options too. There are Points Config and Plot Layout Config as well.

Triplot

Input(s)

  1. Feature table (output of 'Denoise' module)

  2. Taxonomic classification result (output of 'Analysis' module)

  3. Metadata file

    • It will be used to overlay metadata groups on triplot ordination. You may use sample metadata (click here to download)

  4. Environmental metadata file

    • It will be used to project environmental variables onto triplot ordination. You may use sample environmental metadata (click here to download)

Steps

  1. Upload input files triplot input

  2. Choose options triplot step

  3. Start analysis

When it's done running it should look like the following triplot done

  • Feel free to explore other options too. There are Points Config and Plot Layout Config as well.

Bubble plot

Input(s)

  1. Feature table (output of 'Denoise' module)

  2. Taxonomic classification result (output of 'Analysis' module)

  3. Metadata file

    • It will be used to overlay metadata groups on triplot ordination. You may use sample metadata (click here to download)

Steps

  1. Upload input files bubbleplot input

  2. Choose options bubbleplot step

  3. Start analysis

When it's done running it should look like the following bubbleplot done

  • Feel free to explore other options too. There are Points Config and Plot Layout Config as well.
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