Package: CytoSimplex 0.1.1
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:
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')) |
Bug tracker:https://github.com/welch-lab/cytosimplex/issues
Pkgdown:https://welch-lab.github.io
- 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
Last updated 12 months agofrom:8986a8362c. Checks:OK: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 10 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 10 2024 |
Exports:colNormalizeplotBinaryplotQuaternaryplotTernaryselectTopFeaturesshowwriteQuaternaryGIF
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmisc3dmunsellnlmepillarpkgconfigplot3DR6RColorBrewerRcppRcppArmadillorlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Normalize each column of the input matrix by the column sum | colNormalize colNormalize.default colNormalize.dgCMatrix colNormalize.Seurat colNormalize.SingleCellExperiment |
Create binary plots | plotBinary plotBinary.default plotBinary.Seurat plotBinary.simMat plotBinary.SingleCellExperiment |
Create quaternary simplex plots | plotQuaternary plotQuaternary.default plotQuaternary.Seurat plotQuaternary.simMat plotQuaternary.SingleCellExperiment |
Create ternary plots | plotTernary plotTernary.default plotTernary.Seurat plotTernary.simMat plotTernary.SingleCellExperiment |
Major cell type annotation of the example mouse bone marrow data | rnaCluster |
Mouse bone marrow scRNAseq example data | rnaRaw |
Velocity graph of the example mouse bone marrow data | rnaVelo |
Pick top differentially presented features for similarity calculation | selectTopFeatures selectTopFeatures.default selectTopFeatures.Seurat selectTopFeatures.SingleCellExperiment |
Show plist object produced with plot3D package | print.plist show,plist-method |
Create GIF image for dynamic rotating view of 3D quaternary simplex plot | writeQuaternaryGIF |