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

## Documentation for package ‘CytoSimplex’ version 0.2.0

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

## 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 | Craete quaternary simplex plot with Seurat object
plotQuaternary.simMat | Create quaternary simplex plot with pre-calculated similarity matrix
plotQuaternary.SingleCellExperiment | Create quaternary simplex plot with SingleCellExperiment object
plotTernary | Create ternary simplex plots
plotTernary.default | Create ternary simplex plots
plotTernary.Seurat | Create ternary simplex plot with Seurat objects
plotTernary.simMat | Create quaternary simplex plot with pre-calculated similarity matrix
plotTernary.SingleCellExperiment | Create ternary simplex plot with SingleCellExperiment objects
print.quatPlot | Show plist object produced with plot3D package
readH5ADObsNames | Extract 'adata.obs_names' from an H5AD file
readH5ADObsVar | Extract a variable from adata.obs stored in an H5AD file
readH5ADUnsSpMat | Extract a sparse matrix from adata.uns stored in an H5AD file
readVelocytoLoom | Extract the raw counts from a LOOM file
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
writeQuaternaryGIF | Create GIF image for dynamic rotating view of 3D quaternary simplex plot