Package: traviz 1.13.0
Koen Van den Berge
traviz: Trajectory functions for visualization and interpretation.
traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as smoothers estimated by tradeSeq. Furthermore, it allows for visualization of Slingshot trajectories using ggplot2.
Authors:
traviz_1.13.0.tar.gz
traviz_1.13.0.zip(r-4.5)traviz_1.13.0.zip(r-4.4)traviz_1.13.0.zip(r-4.3)
traviz_1.13.0.tgz(r-4.4-any)traviz_1.13.0.tgz(r-4.3-any)
traviz_1.13.0.tar.gz(r-4.5-noble)traviz_1.13.0.tar.gz(r-4.4-noble)
traviz_1.13.0.tgz(r-4.4-emscripten)traviz_1.13.0.tgz(r-4.3-emscripten)
traviz.pdf |traviz.html✨
traviz/json (API)
| # Install 'traviz' in R: |
| install.packages('traviz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:traviz-1.13.0(bioc 3.21)traviz-1.12.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsvisualization
Last updated 23 days agofrom:76fcdb4dfb. Checks:ERROR: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 31 2024 |
| R-4.5-win | ERROR | Oct 31 2024 |
| R-4.5-linux | ERROR | Oct 31 2024 |
| R-4.4-win | ERROR | Oct 31 2024 |
| R-4.4-mac | ERROR | Oct 31 2024 |
| R-4.3-win | ERROR | Oct 31 2024 |
| R-4.3-mac | ERROR | Oct 31 2024 |
Exports:linesplotplotExpressionplotGeneCountplotSmoothers
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemclicolorspacecpp11crayoncurlDelayedArraydigestevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigprincurveR6rappdirsRColorBrewerRcpprglrlangrmarkdownS4ArraysS4VectorssassscalesSingleCellExperimentslingshotSparseArraySummarizedExperimentsystibbletinytexTrajectoryUtilsUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A count matrix, used for testing. | counts |
| A SlingshotDataset object, used for testing. | crv |
| Plot Slingshot output | lines,SlingshotDataSet-method plot,SlingshotDataSet,ANY-method plot-SlingshotDataSet |
| Plot Slingshot output in 3D | plot3d-SlingshotDataSet plot3d.SlingshotDataSet |
| Plot gene expression along pseudotime. | plotExpression plotExpression,matrix,PseudotimeOrdering,character-method plotExpression,matrix,SlingshotDataSet,character-method |
| Plot gene expression in reduced dimension. | plotGeneCount plotGeneCount,SingleCellExperiment-method plotGeneCount,SlingshotDataSet-method |
| Plot the log-transformed counts and the fitted values for a particular gene along all lineages | plotSmoothers plotSmoothers,gam-method plotSmoothers,SingleCellExperiment-method |
| A SingleCellExperiment object, used for testing. | sce |
