module.report.r

R Report Modules

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.

R_Module

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

R_CalculateStats

#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

R_PlotEffectSize

#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

R_PlotMds

#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: