# Simplex Visualization of Cell Fate Similarity in Single-Cell Data

## Documentation for package ‘CytoSimplex’ version 0.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

colNormalize | Normalize each column of the input matrix by the column sum
colNormalize.default | Normalize each column of the input matrix by the column sum
colNormalize.dgCMatrix | Normalize each column of the input matrix by the column sum
colNormalize.Seurat | Normalize each column of the input matrix by the column sum
colNormalize.SingleCellExperiment | Normalize each column of the input matrix by the column sum
plotBinary | Create binary plots
plotBinary.default | Create binary plots
plotBinary.Seurat | Create binary plots
plotBinary.simMat | Create binary plots
plotBinary.SingleCellExperiment | Create binary plots
plotQuaternary | Create quaternary simplex plots
plotQuaternary.default | Create quaternary simplex plots
plotQuaternary.Seurat | Create quaternary simplex plots
plotQuaternary.simMat | Create quaternary simplex plots
plotQuaternary.SingleCellExperiment | Create quaternary simplex plots
plotTernary | Create ternary plots
plotTernary.default | Create ternary plots
plotTernary.Seurat | Create ternary plots
plotTernary.simMat | Create ternary plots
plotTernary.SingleCellExperiment | Create ternary plots
print.plist | Show plist object produced with plot3D package
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
selectTopFeatures | Pick top differentially presented features for similarity calculation
selectTopFeatures.default | Pick top differentially presented features for similarity calculation
selectTopFeatures.Seurat | Pick top differentially presented features for similarity calculation
selectTopFeatures.SingleCellExperiment | Pick top differentially presented features for similarity calculation
show-method | Show plist object produced with plot3D package
writeQuaternaryGIF | Create GIF image for dynamic rotating view of 3D quaternary simplex plot