Hi everybody and @mortonjt
Two things from my gneiss analysis that I would love to have your input on.
1. I wanted to check if I take the right approach in testing my hypothesis and plugging in the right meta-variable in the appropriate command. Basically, I am seeing variation in the microbial community along a soil depth profile and I would like to check several geochemical parameters as metadata if there is some correlation using balances. So, I chose
gradient-clustering because I want to assess the change of balances within a gradient of metadata categories.
qiime gneiss gradient-clustering \ --i-table community_composition.qza \ --m-gradient-file metadata.tsv \ --m-gradient-category "SoilDepth" \ --o-clustering SoilDepth_gc-hierarchy.qza qiime gneiss ilr-transform \ --i-table community_composition.qza \ --i-tree SoilDepth_gc-hierarchy.qza \ --o-balances SoilDepth_gc-balances.qza qiime gneiss ols-regression \ --p-formula "CO2+pH+phosphate" \ --i-table SoilDepth_gc-balances.qza \ --i-tree SoilDepth_gc-hierarchy.qza \ --m-metadata-file metadata.tsv \ --o-visualization regression-summary.qzv
To check what parameter explains the variation along the depth profile most accurately, the sequences were clustered along soil depth, then OLS regression was performed with CO2+pH+phosphate for all of which I have data along the depth gradient. My questions are a) was m-gradient-category “SoilDepth” correctly chosen in the clustering step and b) would I include soil depth in --p-formula as control and c) in the regression summary for the OLS model, what does the “Intercept” represent (mse, Rsquared, R2diff)?
2. With the
balance-taxonomy command I can obtain this nice balance vs. metadata plot. However, it seems that it is possible to only download the pdf of the plot. How would I obtain the coordinates of the data points from the figure?
qiime gneiss balance-taxonomy \ --i-table community_composition.qza \ --i-tree SoilDepth_gc-hierarchy.qza \ --i-taxonomy taxonomy-vsearch.qza \ --p-taxa-level 3 \ --p-balance-name 'y0' \ --m-metadata-file metadata.tsv \ --m-metadata-category pH \ --o-visualization pH_balance-taxa.qzv
One last question: Could somebody explain what exactly the configuration --p-balance-name does?
Thanks for all your help!