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.