Package: CytoSimplex 0.1.1

Yichen Wang

CytoSimplex: Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) <doi:10.1101/2023.12.07.570655> for more details.

Authors:Yichen Wang [aut, cre], Jialin Liu [aut], Joshua Welch [cph]

CytoSimplex_0.1.1.tar.gz
CytoSimplex_0.1.1.tar.gz(r-4.5-noble)CytoSimplex_0.1.1.tar.gz(r-4.4-noble)
CytoSimplex_0.1.1.tgz(r-4.4-emscripten)CytoSimplex_0.1.1.tgz(r-4.3-emscripten)
CytoSimplex.pdf |CytoSimplex.html
CytoSimplex/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/welch-lab/cytosimplex/issues

Pkgdown:https://welch-lab.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • rnaCluster - Major cell type annotation of the example mouse bone marrow data
  • rnaRaw - Mouse bone marrow scRNAseq example data
  • rnaVelo - Velocity graph of the example mouse bone marrow data

2.70 score 3 scripts 183 downloads 7 exports 32 dependencies

Last updated 12 months agofrom:8986a8362c. Checks:OK: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 10 2024
R-4.5-linux-x86_64NOTENov 10 2024

Exports:colNormalizeplotBinaryplotQuaternaryplotTernaryselectTopFeaturesshowwriteQuaternaryGIF

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmisc3dmunsellnlmepillarpkgconfigplot3DR6RColorBrewerRcppRcppArmadillorlangscalestibbleutf8vctrsviridisLitewithr

Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Rendered fromCytoSimplex.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2023-12-16
Started: 2023-12-14

Readme and manuals

Help Manual

Help pageTopics
Normalize each column of the input matrix by the column sumcolNormalize colNormalize.default colNormalize.dgCMatrix colNormalize.Seurat colNormalize.SingleCellExperiment
Create binary plotsplotBinary plotBinary.default plotBinary.Seurat plotBinary.simMat plotBinary.SingleCellExperiment
Create quaternary simplex plotsplotQuaternary plotQuaternary.default plotQuaternary.Seurat plotQuaternary.simMat plotQuaternary.SingleCellExperiment
Create ternary plotsplotTernary plotTernary.default plotTernary.Seurat plotTernary.simMat plotTernary.SingleCellExperiment
Major cell type annotation of the example mouse bone marrow datarnaCluster
Mouse bone marrow scRNAseq example datarnaRaw
Velocity graph of the example mouse bone marrow datarnaVelo
Pick top differentially presented features for similarity calculationselectTopFeatures selectTopFeatures.default selectTopFeatures.Seurat selectTopFeatures.SingleCellExperiment
Show plist object produced with plot3D packageprint.plist show,plist-method
Create GIF image for dynamic rotating view of 3D quaternary simplex plotwriteQuaternaryGIF