q2-SCNIC: Community Tutorial
SCNIC (Sparse Cooccurnce Network Investigation for Compositional data) is a tool for building correlation networks from feature tables, finding modules in said networks and summarizing those modules. Access to all these functionalities is available to qiime2 users via the q2-SCNIC plugin.
The SCNIC method serves three main purposes:
- Making it easy for qiime 2 users to generate correlation networks using a variety of metrics.
- Increasing statistical power by summarizing non-independent features into modules.
- Detecting modules of features which may be of biological interest.
q2-SCNIC: GitHub - shafferm/q2-SCNIC: A QIIME2 plugin for running SCNIC
SCNIC: GitHub - shafferm/SCNIC: Sparse Cooccurence Network Investigation for Compositional data
Installing q2-SCNIC
If you are using qiime 2 2018.8 or later then you must first force an update of your blas version:
conda install -c conda-forge blas=1.1
q2-SCNIC is available via bioconda so installing is easy. Just enter into your qiime 2 conda environment and use this command:
conda install -c lozuponelab q2-SCNIC
That's it.
Note: This adds a few additional packages into your qiime 2 environment. Let us know if this affects your usage of qiime 2 by raising an issue here or by posting on the qiime 2 forum. You also can install a new qiime 2 environment and install q2-SCNIC there to avoid any conflicts with already installed plugins.
Getting data for q2-SCNIC
To run q2-SCNIC you need to start with a Feature table. You can do this tutorial with one of your own that you have imported or generate with qiime 2 or with a sample one. If you already have a feature table to start with you can skip to Running q2-SCNIC.
Downloading an example feature table
Use this command to download a sample feature table for analysis with q2-SCNIC.
wget https://github.com/shafferm/q2-SCNIC/raw/master/tests/data/fake_data.biom
Then import this table into qiime 2 using this command.
qiime tools import \
--input-path fake_data.biom \
--type 'FeatureTable[Frequency]' \
--input-format BIOMV210Format \
--output-path fake_data.qza
Now you have a filtered .qza file of your feature table to run q2-SCNIC.
Running q2-SCNIC
SCNIC can be broken up into three main steps:
- Filtering your data so that it is useful for correlation analysis
- Making a correlation table and network
- Finding modules in the correlation network
We will run through these steps with the fake_data.qza generated above but you can run it with any feature table by changing the name of fake_data.qza to whatever your qza is called.
1. Filtering your data
Correlational analyses are hampered by having large numbers of zeroes. Therefore we are first going to remove these from our data. In the q2-SCNIC plugin a method called sparcc-filter to do this based on the parameters used in Friedman et al. This method removes all samples with a feature abundance total below 500 and all features with an average abundance less than 2 across all samples. You do not need to use these parameters and can use any method you chose to do this. Other methods for filtering feature tables are outlined here.
To use the sparcc filter use this command:
qiime SCNIC sparcc-filter \
--i-table fake_data.qza \
--o-table-filtered fake_data-filtered.qza
2. Calculating correlations and making your network
With your filtered data you can calculate your correlation table and make a network to visualize your correlations.
Generating a correlation table
To calculate all pairwise correlations between features in your filtered table use the following command:
qiime SCNIC calculate-correlations \
--i-table fake_data-filtered.qza \
--p-method sparcc \
--o-correlation-table fake_correls.qza
Here we use the sparCC metric for measuring the strength of our correlation. This metric is recommended when you data is in the form of OTUs or ASVs (Weiss et al. 2017). You may also use Pearson, Spearman or Kendall-Tau correlation.
(Optional) Making a correlation network
From fake_correls.qza we can generate a network based on a minimum R value cutoff. A cooccurence network (AKA a network with only positive edges) will also be generated when finding modules. If you only want to make a network and not find modules or build a network with both positive and negative correlations then you can use this command:
qiime SCNIC build-correlation-network-r \
--i-correlation-table fake_correls.qza \
--p-min-val .35 \
--o-correlation-network fake_net.qza
The --r-min-val parameter sets the minimum R value required to call a correlation between two features significant and therefore draw an edge between them. In this example we used a minimum value of .35. This is a common cutoff used with the sparCC correlation metric when used with 16S data.
If you want to make a correlation network based on a maximum significant p-value using the build-correlation-network-p method.
3. Detecting and summarizing modules of features
Areas of a network which are strongly interconnected are called modules. With this step we detect these modules and summarize the features in them. The summarization is a simple sum of all features in your modules across samples. This makes it so that sample abundance counts remain the same after summarization and therefore this table can be used for further statistical tests like ANCOM for testing for differential abundance.
To detect and summarize modules use this command:
qiime SCNIC make-modules-on-correlations \
--i-correlation-table fake_correls.qza \
--i-feature-table fake_data.qza \
--p-min-r .35 \
--o-collapsed-table fake_data.collapsed.qza \
--o-correlation-network fake_net.modules.qza \
--o-module-membership fake_membership.qza
The fake_data.collapsed.qza is a feature table you can use with any further non-phylogenetic analysis. fake_net.modules.qza is a network that is annotated with correlation information as well as module membership and can be exported from the .qza to visualize with tools such as Cytoscape.
The fake_membership.qza is viewable as metadata and can be turned into a visualization via this command:
qiime metadata tabulate \
--m-input-file fake_membership.qza \
--o-visualization fake_membership.qzv
This visualization can then be used to see what features are in each module.
With that you have ran SCNIC and have a feature table with fewer features giving you more power for further analyses and a correlation network investigate correlations between features in your community of interest.
