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'))

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

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 208 downloads 7 exports 32 dependencies

Last updated 11 months agofrom:8986a8362c. Checks:OK: 1 NOTE: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 11 2024
R-4.5-linux-x86_64	NOTE	Oct 11 2024

Exports:colNormalize plotBinary plotQuaternary plotTernary selectTopFeatures show writeQuaternaryGIF

Dependencies:cli colorspace fansi farver ggplot2 glue gtable isoband labeling lattice lifecycle magrittr MASS Matrix mgcv misc3d munsell nlme pillar pkgconfig plot3D R6 RColorBrewer Rcpp RcppArmadillo rlang scales tibble utf8 vctrs viridisLite withr

Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Yichen Wang, Jialin Liu

Rendered fromCytoSimplex.Rmdusingknitr::rmarkdownon Oct 11 2024.

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

Citation

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