Simplex Visualization of Cell Fate Similarity in Single-Cell Data

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Documentation for package ‘CytoSimplex’ version 0.1.1

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