tSNEVisualization: Visualization of marker proteins by t-SNE map

In TanerArslan/SubCellBarCode-R-Package: 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])

r.markers <- markerQualityControl(c.prots, df)

tsneMap.df <- tsneVisualization(protein.data = df,
markerProteins = r.markers,
dims = 3, theta = c(0.4), perplexity = c(50))
}

TanerArslan/SubCellBarCode-R-Package documentation built on May 14, 2019, 9:38 a.m.