R_PlotOtus#

Add to module run order:
#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

Properties#

Properties are the name=value pairs in the configuration file.

R_PlotOtus properties:#

Property	Description
r.pValFormat	string Sets the format used in R sprintf() function default: %1.2g
r_PlotOtus.customScript	file path Path to a custom R script to use in place of the built-in module script. 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.colorBase	string base color used for labels & headings in the PDF report; Must be a valid color in R. default: black
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.colorHighlight	string color is used to highlight significant OTUs in plot default: red
r.colorPalette	string palette argument passed to get_palette {ggpubr} to select colors for some output visualiztions default: null
r.colorPoint	string default color of scatterplot and strip-chart plot points default: black
r.debug	boolean Options: Y/N. If Y, will generate R Script log files default: Y
r.pch	integer Sets R plot pch parameter for PDF report default: 21
r.rareOtuThreshold	numeric If >=1, R will filter OTUs found in fewer than this many samples. If <1, R will interperate the value as a percentage and discard OTUs not found in at least that percentage of samples default: 1
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
pipeline-dependent
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_PlotOtus.imageOwner
R_PlotOtus.imageName
R_PlotOtus.imageTag

Citation#

BioLockJ v1.4.2
Module created by Mike Sioda and developed by Ivory Blakley