tsneVisualization {SubCellBarCode} | R Documentation |
The marker proteins are visualized in 3D t-SNE map to see the distributions of the marker proteins.
tsneVisualization(protein.data, markerProteins, dims, theta, perplexity)
protein.data |
data.frame; fractionated proteomics data |
markerProteins |
character; robust marker proteins, gene symbols, that are present in the given data and overlapped with package's marker protein list. |
dims |
integer; dimensionality |
theta |
numeric; Speed/accuracy trade-off ,increase for less accuracy |
perplexity |
integer; Perplexity parameter |
tsneMap.df
{ df <- loadData(SubCellBarCode::hcc827Ctrl) c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1]) set.seed(21) tsneMap.df <- tsneVisualization(protein.data = df, markerProteins = c.prots[1:20], dims = 2, theta = c(0.4), perplexity = c(5)) }