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Diana edited this page Feb 6, 2020 · 1 revision

Install

To install from conda,

conda install -c dianahaider/q2-compare

To install from this repository, clone the repos in your computer then cd to the main directory q2-comp

python setup.py install

CHAOS! Clustering Helper: ASVs and OTUs Scrutinized

Clustering, or denoising of high-throughput sequencing can get confusing because of the diversity of parameters, and methods! 😥 🤯 Compare quantifies differences between methods and is a visual exploration tool for your post-clustering or post-denoising data.


CHAOS conducts pairwise comparisons of alpha diversity or frequency tables, and comparisons of denoising statistics.
All visualizations can be tweaked by preferences for color palette, style and context.

tutorial_V1

Alpha

Feature tables of frequency or alpha diversity indices artifacts can be compared through three visualizations and one table. The pairwise plot shows the correlation between each pair of samples between each method, and the density plot of each method is displaned in the diagonale. The raincloud plot shows both the density plot and a box plot for each method.

All plots can be colored by a categorical metadata column, the palette of colors can be changed, the style and context of the plot can also be specified optionally. Labels can also be provided to identify each input table.

Cool trick: it can also produce simpler visualizations such as box plots or violin plots if that's your preference. All plots can be colored by categorical metadata colummns, but this is optional.

qiime comp alpha-frequency \
  --i-tables table1.qza table2.qza table3.qza \
  --m-metadata METADATA.txt \
  --p-metadata-col depth \
  --p-labels DADA2_maxee1 DADA2_maxee2 DADA2_maxee3
  --o-visualization visualization_frequency.qzv

Output artifacts:

qiime comp alpha-index \
  --i-alpha-diversity-index shannon1.qza shannon2.qza shannon3.qza \
  --m-metadata METADATA.txt \
  --p-metadata-col depth \
  --o-visualization visualization_index.qzv

Output artifacts:

And just def

qiime comp alpha-core \
  --i-tables table1.qza table2.qza table3.qza \
  --i-alpha-diversity shannon1.qza shannon2.qza shannon3.qza \
  --m-metadata METADATA.txt \
  --p-metadata-col depth \
  --o-visualization visualization_index.qzv
  --o-visualization visualization_frequency.qzv
  --o-visualization visualization_merged.qzv

Output artifacts:

Denoise

This functions xyz Blblalblablalbalblabla

qiime comp denoise \
  --i-stats stats1.qza stats.qza stats.qza \
  --p-labels Method1 Method2 Method3
  --o-visualization visualization.qzv

Output artifacts:

Taxonomy

This functions xyz Blblalblablalbalblabla

qiime compare taxo-variability \
  --i-stats stats1.qza stats.qza stats.qza \
  --p-labels Method1 Method2 Method3
  --o-visualization visualization.qzv

Output artifacts:

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