Package: toxpiR 1.3.2

Jonathon F Fleming

toxpiR: Create ToxPi Prioritization Models

Enables users to build 'ToxPi' prioritization models and provides functionality within the grid framework for plotting ToxPi graphs. 'toxpiR' allows for more customization than the 'ToxPi GUI' (<https://toxpi.github.io/>) and integration into existing workflows for greater ease-of-use, reproducibility, and transparency. toxpiR package behaves nearly identically to the GUI; the package documentation includes notes about all differences. The vignettes download example files from <https://github.com/ToxPi/ToxPi-example-files>.

Authors:Jonathon F Fleming [aut, cre], Dayne L Filer [aut, fnd], Dillon T Lloyd [aut], Preethi Thunga [aut], Skylar W Marvel [aut], Alison A Motsinger-Reif [fnd], David M Reif [aut, fnd]

toxpiR_1.3.2.tar.gz
toxpiR_1.3.2.zip(r-4.7)toxpiR_1.3.2.zip(r-4.6)toxpiR_1.3.2.zip(r-4.5)
toxpiR_1.3.2.tgz(r-4.6-any)toxpiR_1.3.2.tgz(r-4.5-any)
toxpiR_1.3.2.tar.gz(r-4.7-any)toxpiR_1.3.2.tar.gz(r-4.6-any)
toxpiR_1.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
toxpiR/json (API)

# Install 'toxpiR' in R:
install.packages('toxpiR', repos = c('https://toxpi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/toxpi/toxpir/issues

Pkgdown/docs site:https://toxpi.github.io

Datasets:

On CRAN:

Conda:

data-sciencemodelingtoxicology

6.84 score 11 stars 26 scripts 658 downloads 39 exports 31 dependencies

Last updated from:4d20bb5637. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK175
source / vignettesOK285
linux-release-x86_64OK175
macos-release-arm64OK161
macos-oldrel-arm64OK181
windows-develOK115
windows-releaseOK117
windows-oldrelOK114
wasm-releaseOK139

Exports:as.data.frameas.TxpModelListas.TxpResultListas.TxpSliceListas.TxpTransFuncListduplicatedgrid.pieGridGrobgrid.pieGrobmergepieGridGrobpieGrobplotsorttxpCalculateScorestxpExportGuitxpIDstxpIDs<-txpImportGuitxpMissingtxpModelTxpModelTxpModelListtxpRanksTxpResultListtxpResultParamtxpScoresTxpSliceTxpSliceListtxpSlicestxpSlices<-txpSliceScoresTxpTransFuncTxpTransFuncListtxpTransFuncstxpTransFuncs<-txpValueNamestxpValueNames<-txpWeightstxpWeights<-

Dependencies:BiocGenericsclicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS4VectorsS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Export ToxPi GUI Files
Key differences between Java GUI and toxpiR | Slice weights | Transformation/scaling functions | Metrics in multiple slices | Example use | Compare the data files | Compare results
Rendered fromexportToGui.rmdusingknitr::rmarkdown

Last update: 2025-12-16
Started: 2022-07-20

Import ToxPi GUI Files
Rendered fromimportFromGui.Rmdusingknitr::rmarkdown

Last update: 2025-12-16
Started: 2022-02-02

toxpiR Introduction
Introduction | What is ToxPi? | Outline | Installation | Standard installation | Installation from GitHub | Launching package in R | Flowchart | Example usage | Load the dataset | Specify slice information | TxpSlice(txpValueNames, txpTransFuncs) | TxpSliceList() | Create ToxPi model | TxpModel() | Calculate ToxPi scores | txpCalculateScores() | Visualization | ggplot Method | Default plot | Coloration Options | Binary Options | Format/Theme Options | pieGrob Method | ggplot vs grid Comparison | Citation
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2025-12-16
Started: 2022-02-02

Readme and manuals

Help Manual

Help pageTopics
Create a filled-box legendboxLegendGrob
Make grid of pieGrobsgrid.pieGridGrob pieGridGrob
Create a pie grobgrid.pieGrob pieGrob
toxpiR data objectstoxpiR-datasets txp_example_input txp_example_model
Calculate ToxPi Scores for the given model and input datatxpCalculateScores txpCalculateScores,list,data.frame-method txpCalculateScores,TxpModel,data.frame-method txpCalculateScores,TxpModelList,data.frame-method
Export comma-separated file intended for ToxPi GUItxpExportGui
toxpiR package genericstxpGenerics txpIDs txpIDs<- txpMissing txpModel txpRanks txpResultParam txpScores txpSlices txpSlices<- txpSliceScores txpTransFuncs txpTransFuncs<- txpValueNames txpValueNames<- txpWeights txpWeights<-
Import data file generated by ToxPi GUItxpImportGui
ToxPi Modellength,TxpModel-method merge,TxpModel,TxpModel-method names,TxpModel-method names<-,TxpModel-method TxpModel TxpModel-class TxpModel-txpSlices txpSlices,TxpModel-method txpSlices<-,TxpModel-method txpTransFuncs,TxpModel-method txpTransFuncs<-,TxpModel-method txpValueNames,TxpModel-method txpWeights,TxpModel-method txpWeights<-,TxpModel-method
List of TxpModel objectsas.TxpModelList duplicated,TxpModelList-method TxpModelList TxpModelList-class
ToxPi Resultas.data.frame,TxpResult-method length,TxpResult-method names,TxpResult-method names<-,TxpResult-method sort,TxpResult-method txpIDs,TxpResult-method txpIDs<-,TxpResult-method txpMissing,TxpResult-method txpModel,TxpResult-method txpRanks,TxpResult-method TxpResult TxpResult-class txpResultParam,TxpResult-method txpScores,TxpResult-method txpSlices,TxpResult-method txpSliceScores,TxpResult-method txpTransFuncs,TxpResult-method txpValueNames,TxpResult-method txpWeights,TxpResult-method [,TxpResult,character,missing-method [,TxpResult,integer,missing-method [,TxpResult,logical,missing-method [,TxpResult,numeric,missing-method
Plot TxpResult objectsplot plot,TxpResult,missing-method plot,TxpResult,numeric-method TxpResult-plot
List of TxpResult objectsas.TxpResultList duplicated,TxpResultList-method TxpResultList TxpResultList-class
ToxPi Result ParametersTxpResultParam TxpResultParam-class
ToxPi Slicelength,TxpSlice-method merge,TxpSlice,TxpSlice-method TxpSlice TxpSlice-class txpTransFuncs,TxpSlice-method txpTransFuncs<-,TxpSlice-method txpValueNames,TxpSlice-method txpValueNames<-,TxpSlice-method
List of TxpSlice objectsas.TxpSliceList duplicated,TxpSliceList-method TxpSliceList TxpSliceList-class txpTransFuncs,TxpSliceList-method txpValueNames,TxpSliceList-method
Numeric transformation functionTxpTransFunc TxpTransFunc-class
List of TxpTransFunc objectsas.TxpTransFuncList TxpTransFuncList TxpTransFuncList-class