r properties#
These properties are directed to R modules.
| Property | Description |
|---|---|
| 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.excludeFields | list Fields from the metadata that will be excluded from any auto-determined typing, or plotting; R reports must contain at least one valid nominal or numeric metadata field. default: null |
| r.nominalFields | list Override default property type by explicitly listing it as nominal. default: null |
| r.numericFields | list Override default property type by explicitly listing it as numeric. default: null |
| r.pch | integer Sets R plot pch parameter for PDF report default: 21 |
| r.pvalCutoff | numeric p-value cutoff used to assign label r.colorHighlight default: 0.05 |
| 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.reportFields | list Metadata fields to include in reports; Fields listed here must exist in the metadata file. R reports must contain at least one valid field. default: null |
| 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 |
| r.useUniqueColors | boolean force to use a unique color for every value in every field plotted; only recommended for low numbers of metadata columns/values. default: null |
Several plotting options are available.