Package: q2-dbbact
q2-dbbactAQiime2plugin fordbBactFeatures:Differential abundance testing usingCalourrank-mean differential abundance test (withdsFDRcorrection).dbBact term enrichment from differntial abundance results of qiime2 (i.e. songbird/q2-aldex2/ancom/dacomp or the built in rank-mean test).Create a wordcloud of dbBact terms for a given feature table.Generate an interactive heatmap visualization for a feature table. The heatmap provides links to dbBact annotations for each ASV.Generate Venn diagram for a differential abundance result and a given dbBact term.Background dbBact term enrichment analysis for experiments without controls (i.e. what terms are enriched in the bacteria in a given feature table compared to all dbBact experiments of a given type).Examples:Run the q2-dbBact enrichment pipeline for a given feature table:Our input is a feature table and a metadata file with a given column dividing our samples into two groups.q2-dbBact will detect ASVs different between the two groups, and identify dbBact terms enriched in one of the two groups compared to the otherqiime dbbact enrich-pipeline --i-table cfs-merged.qza --m-metadata-file map.cfs.txt --p-field Subject --output-dir cfs-pipelineDraw an interactive heatmapThis creates a zoomable heatmap with a list of dbBact annotation for each bacteria that is clicked. Useful for exploring your sequencing results and getting a feeling for what is going on (contaminations, bacterial sources, groups of samples, etc.)Our input is a feature table and a metadata file with a given column dividing our samples into two groups.qiime dbbact heatmap --i-table cfs-table.qza --i-repseqs cfs-rep-seqs.qza --i-taxonomy cfs-taxonomy.qza --m-metadata-file map.cfs.txt --p-sort-field Subject --o-visualization heatmap-cfsDraw a dbBact terms wordcloud for the set of bacteria in a feature-tableThe wordcloud is created for all the bacteria in the feature table.The output wordcloud words are dbBact terms associated with the bacteria. The word size corresponds to the F-score (recall and precision) of the term. Blue terms are positively associated (i.e. appear in COMMON/DOMINANT/HIGHER IN annotations) where as red terms (preceeded by a "-") are negatively associated (i.e. appear in LOWER IN annotations).qiime dbbact draw-wordcloud-vis --i-data cfs-table.qza --i-repseqs cfs-rep-seqs.qza --o-visualization wordcloud-cfsIdentify differentially abundant bacteria between two sample groupsq2-dbBact utilizes the non-parametric (permutation based) Calour diff_abundance() function. By default it uses a rank-mean test with dsFDR multiple hypothesis correction.The test can also be performed as a paired test using an additional metadata pair-field (permutations are performed only between samples sharing the same pair-field value).qiime dbbact diff-abundance --i-table cfs-merged.qza --m-metadata-file map.cfs.txt --p-field Subject --p-alpha 0.1 --p-val1 Patient --p-val2 Control --o-diff diff-cfs-dsfdrIdentify and plot enriched dbBact terms between two groups of bacteriaPerformed on the output of a differential-abundance test. q2-dbBact supports the following formats:songbirdancomq2-aldex2dbBact diff-abundanceany tsv fileThis command identifies dbBact terms the are significantly more associated with bacteria from one group compared to the otherqiime dbbact enrichment --i-diff diff-cfs-dsfdr.qza --p-source dsfdr --o-enriched enriched-cfs-dsfdrThe output can be visualized (and the complete table saved) using the visualization command:qiime dbbact plot-enrichment --i-enriched enriched-cfs-dsfdr.qza --o-visualization barplot-enriched-cfs-dsfdr --p-labels CFS ControlVenn diagram for examining term distribution in the two groupsInput is the results of a differential abundance analysis (which provides two ASV groups - positive and negative effect size), and a dbBact term.The venn diagram shows how many of the ASVs in each group have the term, as well as how many total dbBact ASVs have the term associated.qiime dbbact venn --i-diff diff-cfs-dsfdr.qza --p-terms "small village" --p-source dsfdr --p-label1 Control --p-label2 CFS --o-visualization venn-cfs-human-village