Modules in the biolockj.module.report.r sub-package generate the statistical analysis and visualizations by executing R scripts. The statistical analysis is performed on the taxa abundance tables generated by AddMetadataToTaxaTables.

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cannot be included in the pipeline run order

Description: Abstract implementation of ScriptModule that other R modules extend to inherit standard R script functionality. Abstract modules cannot be included in the pipeline run order.

Options:

• exe.rScript
• r.debug
• r.nominalFields
• r.numericFields
• r.rareOtuThreshold
• r.reportFields
• r.saveRData
• r.timeout
• report.numHits
• report.numReads
• report.taxonomyLevel

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#BioModule biolockj.module.report.r.R_CalculateStats

Description: Generate a summary statistics table with [adjusted and unadjusted] [parameteric and non-parametirc] p-values and r² values for each reportable metadata field and each report.taxonomyLevel configured.

Options:

• r_CalculateStats.pAdjustMethod
• r_CalculateStats.pAdjustScope

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#BioModule biolockj.module.report.r.R_PlotEffectSize

Description: Generate horizontal barplot representing effect size (Cohen's d, r², and/or fold change) for each reportable metadata field and each report.taxonomyLevel configured.

Options:

• r_PlotEffectSize.parametricPval
• r_PlotEffectSize.disablePvalAdj
• r_PlotEffectSize.excludePvalAbove
• r_PlotEffectSize.taxa
• r_PlotEffectSize.maxNumTaxa
• r_PlotEffectSize.disableCohensD
• r_PlotEffectSize.disableRSquared
• r_PlotEffectSize.disableFoldChange
• r.colorHighlight
• r.pvalCutoff

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#BioModule biolockj.module.report.r.R_PlotMds

Description: Generate sets of multidimensional scaling plots showing 2 axes at a time (up to the <r_PlotMds.numAxis>th axis) with color coding based on each categorical metadata field (default) or by each field given in r_PlotMds.reportFields.

Options:

• r_PlotMds.numAxis
• r_PlotMds.reportFields
• r_PlotMds.distance
• r.colorPalette
• r.colorPoint
• r.pch
• r.pvalCutoff
• r.pValFormat

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#BioModule biolockj.module.report.r.R_PlotOtus

Description: Generate OTU-metadata box-plots and scatter-plots for each reportable metadata field and each report.taxonomyLevel configured

Options:

• r.colorBase
• r.colorHighlight
• r.colorPalette
• r.colorPoint
• r.pch
• r.pvalCutoff
• r.rareOtuThreshold
• r.pValFormat

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#BioModule biolockj.module.report.r.R_PlotPvalHistograms

Description: Generate p-value histograms for each reportable metadata field and each report.taxonomyLevel configured

Options:

• r.pvalCutoff

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