tsneVisualization: Visualization of marker proteins by t-SNE map

In SubCellBarCode: SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Description

The marker proteins are visualized in 3D t-SNE map to see the distributions of the marker proteins.

Usage

tsneVisualization(protein.data, markerProteins, dims, theta, perplexity)

Arguments

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

Value

tsneMap.df

Examples

{

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))
}

SubCellBarCode documentation built on Nov. 8, 2020, 5:26 p.m.