Function reference

All functions

colNormalize()

Normalize each column of the input matrix by the column sum

plotBinary()

Create binary plots

plotQuaternary()

Create quaternary simplex plots

plotQuaternary(<Seurat>)

Craete quaternary simplex plot with Seurat object

plotQuaternary(<SingleCellExperiment>)

Create quaternary simplex plot with SingleCellExperiment object

plotQuaternary(<simMat>)

Create quaternary simplex plot with pre-calculated similarity matrix

plotTernary()

Create ternary simplex plots

plotTernary(<Seurat>)

Create ternary simplex plot with Seurat objects

plotTernary(<SingleCellExperiment>)

Create ternary simplex plot with SingleCellExperiment objects

plotTernary(<simMat>)

Create quaternary simplex plot with pre-calculated similarity matrix

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

writeQuaternaryGIF()

Create GIF image for dynamic rotating view of 3D quaternary simplex plot