Package: traviz 1.11.0

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:Hector Roux de Bezieux [aut, ctb], Kelly Street [aut, ctb], Koen Van den Berge [aut, cre]

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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'))

Peer review:

Datasets:
  • counts - A count matrix, used for testing.
  • crv - A SlingshotDataset object, used for testing.
  • sce - A SingleCellExperiment object, used for testing.

On BioConductor:traviz-1.11.0(bioc 3.20)traviz-1.10.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

5 exports 0.61 score 83 dependencies

Last updated 2 months agofrom:0b9debea59

Exports:linesplotplotExpressionplotGeneCountplotSmoothers

Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemclicolorspacecpp11crayoncurlDelayedArraydigestevaluatefansifarverfastmapfontawesomefsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigprincurveR6rappdirsRColorBrewerRcpprglrlangrmarkdownS4ArraysS4VectorssassscalesSingleCellExperimentslingshotSparseArraySummarizedExperimentsystibbletinytexTrajectoryUtilsUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXVectoryamlzlibbioc

Using ggplot2 with slingshot

Hector Roux de Bézieux and Kelly Street

Rendered fromslingshot.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2021-06-18
Started: 2021-06-09

Using traviz

Koen Van den Berge, Hector Roux de Bézieux, Kelly Street

Rendered fromtraviz.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2021-08-02
Started: 2021-08-02

Readme and manuals

Help Manual

Help pageTopics
A count matrix, used for testing.counts
A SlingshotDataset object, used for testing.crv
Plot Slingshot outputlines,SlingshotDataSet-method plot,SlingshotDataSet,ANY-method plot-SlingshotDataSet
Plot Slingshot output in 3Dplot3d-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 lineagesplotSmoothers plotSmoothers,gam-method plotSmoothers,SingleCellExperiment-method
A SingleCellExperiment object, used for testing.sce