tsneVisualization {SubCellBarCode} | R Documentation

## Visualization of marker proteins by t-SNE map

### 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))
    }

[Package SubCellBarCode version 1.2.6 Index]