R_PlotEffectSize#
Add to module run order:
#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.
Properties#
Properties are the name=value pairs in the configuration file.
R_PlotEffectSize properties:#
| Property | Description |
|---|---|
| r_PlotEffectSize.customScript | file path Path to a custom R script to use in place of the built-in module script. default: null |
| r_PlotEffectSize.disableCohensD | boolean Options: Y/N. If N (default), produce plots for binary attributes showing effect size calculated as Cohen's d. If Y, skip this plot type. default: null |
| r_PlotEffectSize.disableFoldChange | boolean Options: Y/N. If N (default), produce plots for binary attributes showing the fold change. If Y, skip this plot type. default: Y |
| r_PlotEffectSize.disablePvalAdj | boolean Options: Y/N. If Y, the non-adjusted p-value is used when determining which taxa to include in the plot and which should get a (). If N (default), the adjusted p-value is used. default: null* |
| r_PlotEffectSize.disableRSquared | boolean Options: Y/N. If N (default), produce plots showing effect size calculated as the r-squared value. If Y, skip this plot type. default: null |
| r_PlotEffectSize.excludePvalAbove | numeric Options: [0,1], Taxa with a p-value above this value are excluded from the plot. default: 1 |
| r_PlotEffectSize.maxNumTaxa | integer Each plot is given one page. This is the maximum number of bars to include in each one-page plot. default: 40 |
| r_PlotEffectSize.parametricPval | boolean Options: Y/N. If Y, the parametric p-value is used when determining which taxa to include in the plot and which should get a (). If N (default), the non-parametric p-value is used. default: null* |
| r_PlotEffectSize.taxa | list Override other criteria for selecting which taxa to include in the plot by specifying wich taxa should be included default: null |
General properties applicable to this module:#
| Property | Description |
|---|---|
| cluster.batchCommand | string Terminal command used to submit jobs on the cluster default: null |
| cluster.jobHeader | string Header written at top of worker scripts default: null |
| cluster.modules | list List of cluster modules to load at start of worker scripts default: null |
| cluster.prologue | string To run at the start of every script after loading cluster modules (if any) default: null |
| cluster.statusCommand | string Terminal command used to check the status of jobs on the cluster default: null |
| docker.saveContainerOnExit | boolean If Y, docker run command will NOT include the --rm flag default: null |
| docker.verifyImage | boolean In check dependencies, run a test to verify the docker image. default: null |
| exe.Rscript | executable Path for the "Rscript" executable; if not supplied, any script that needs the Rscript command will assume it is on the PATH. default: null |
| pipeline.defaultStatsModule | string Java class name for default module used generate p-value and other stats default: biolockj.module.report.r.R_CalculateStats |
| r.colorFile | file path path to a tab-delimited file giving the color to use for each value of each metadata field plotted. default: null |
| r.debug | boolean Options: Y/N. If Y, will generate R Script log files default: Y |
| r.saveRData | boolean If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData" default: null |
| r.timeout | integer defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used. default: 0 |
| script.defaultHeader | string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash |
| script.numThreads | integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8 |
| script.numWorkers | integer Set number of samples to process per script (if parallel processing) default: 1 |
| script.permissions | string Used as chmod permission parameter (ex: 774) default: 770 |
| script.timeout | integer Sets # of minutes before worker scripts times out. default: null |
Details#
version: 0.0.0 none
Adds modules#
pre-requisite modules
biolockj.module.report.r.R_CalculateStats
post-requisite modules
none found
Docker#
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/r_module:v1.3.18
This can be modified using the following properties:
R_PlotEffectSize.imageOwner
R_PlotEffectSize.imageName
R_PlotEffectSize.imageTag
Citation#
BioLockJ v1.4.2
Module developed by Ivory Blakley.