Package: toxpiR 1.3.0
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.org>) 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:
toxpiR_1.3.0.tar.gz
toxpiR_1.3.0.zip(r-4.5)toxpiR_1.3.0.zip(r-4.4)toxpiR_1.3.0.zip(r-4.3)
toxpiR_1.3.0.tgz(r-4.4-any)toxpiR_1.3.0.tgz(r-4.3-any)
toxpiR_1.3.0.tar.gz(r-4.5-noble)toxpiR_1.3.0.tar.gz(r-4.4-noble)
toxpiR_1.3.0.tgz(r-4.4-emscripten)toxpiR_1.3.0.tgz(r-4.3-emscripten)
toxpiR.pdf |toxpiR.html✨
toxpiR/json (API)
NEWS
| # 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
- txp_example_input - ToxpiR data objects
- txp_example_model - ToxpiR data objects
data-sciencemodelingtoxicology
Last updated 3 months agofrom:4693c68ef5. Checks:OK: 6 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 02 2024 |
| R-4.5-win | OK | Nov 02 2024 |
| R-4.5-linux | WARNING | Nov 02 2024 |
| R-4.4-win | OK | Nov 02 2024 |
| R-4.4-mac | OK | Nov 02 2024 |
| R-4.3-win | OK | Nov 02 2024 |
| R-4.3-mac | OK | Nov 02 2024 |
Exports:as.data.frameas.TxpModelListas.TxpResultListas.TxpSliceListas.TxpTransFuncListduplicatedgrid.pieGridGrobgrid.pieGrobmergepieGridGrobpieGrobplotsorttxpCalculateScorestxpExportGuitxpIDstxpIDs<-txpImportGuitxpMissingtxpModelTxpModelTxpModelListtxpRanksTxpResultListtxpResultParamtxpScoresTxpSliceTxpSliceListtxpSlicestxpSlices<-txpSliceScoresTxpTransFuncTxpTransFuncListtxpTransFuncstxpTransFuncs<-txpValueNamestxpValueNames<-txpWeightstxpWeights<-
Dependencies:BiocGenericsclicodetoolscolorspacecpp11crayondplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclelobstrmagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitspryrpurrrR6RColorBrewerRcpprlangS4Vectorsscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Export ToxPi GUI Files
Rendered fromexportToGui.rmdusingknitr::rmarkdownon Nov 02 2024.Last update: 2022-07-20
Started: 2022-07-20
Import ToxPi GUI Files
Rendered fromimportFromGui.Rmdusingknitr::rmarkdownon Nov 02 2024.Last update: 2022-07-20
Started: 2022-02-02
toxpiR Introduction
Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 02 2024.Last update: 2024-08-29
Started: 2022-02-02
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create a filled-box legend | boxLegendGrob |
| Make grid of pieGrobs | grid.pieGridGrob pieGridGrob |
| Create a pie grob | grid.pieGrob pieGrob |
| toxpiR data objects | toxpiR-datasets txp_example_input txp_example_model |
| Calculate ToxPi Scores for the given model and input data | txpCalculateScores txpCalculateScores,list,data.frame-method txpCalculateScores,TxpModel,data.frame-method txpCalculateScores,TxpModelList,data.frame-method |
| Export comma-separated file intended for ToxPi GUI | txpExportGui |
| toxpiR package generics | txpGenerics txpIDs txpIDs<- txpMissing txpModel txpRanks txpResultParam txpScores txpSlices txpSlices<- txpSliceScores txpTransFuncs txpTransFuncs<- txpValueNames txpValueNames<- txpWeights txpWeights<- |
| Import data file generated by ToxPi GUI | txpImportGui |
| ToxPi Model | length,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 objects | as.TxpModelList duplicated,TxpModelList-method TxpModelList TxpModelList-class |
| ToxPi Result | as.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 objects | plot plot,TxpResult,missing-method plot,TxpResult,numeric-method TxpResult-plot |
| List of TxpResult objects | as.TxpResultList duplicated,TxpResultList-method TxpResultList TxpResultList-class |
| ToxPi Result Parameters | TxpResultParam TxpResultParam-class |
| ToxPi Slice | length,TxpSlice-method merge,TxpSlice,TxpSlice-method TxpSlice TxpSlice-class txpTransFuncs,TxpSlice-method txpTransFuncs<-,TxpSlice-method txpValueNames,TxpSlice-method txpValueNames<-,TxpSlice-method |
| List of TxpSlice objects | as.TxpSliceList duplicated,TxpSliceList-method TxpSliceList TxpSliceList-class txpTransFuncs,TxpSliceList-method txpValueNames,TxpSliceList-method |
| Numeric transformation function | TxpTransFunc TxpTransFunc-class |
| List of TxpTransFunc objects | as.TxpTransFuncList TxpTransFuncList TxpTransFuncList-class |
