plotBarcode {SubCellBarCode} | R Documentation

## Visualize the SubCellBarCode

### Description

Stacked bar plot are plotted for compartment and neighborhood level with respect to classification probabilities.

### Usage

    plotBarcode(sampleClassification, protein, s1PSM)

### Arguments

`sampleClassification` | data.frame; merged classification, combination of compartment and neighborhood classification.
`protein` | character; protein gene symbol name
`s1PSM` | data.frame; minimum PSM count table. Row names should be gene centric protein id.

### Value

proteinPlot

### Examples

    {

    #create mock data
    plot.df <- data.frame(Protein = "TP53",
    NeighborhoodCls = "Nuclear",
    CompartmentCls = "N1",
    Secretory = as.numeric(0.01),
    Nuclear = as.numeric(0.95),
    Cytosol = as.numeric(0.02),
    Mitochondria = as.numeric(0.02),
    S1 = as.numeric(0.02),
    S2 = as.numeric(0.02),
    S3 = as.numeric(0.02),
    S4 = as.numeric(0.02),
    N1 = as.numeric(0.72),
    N2 = as.numeric(0.02),
    N3 = as.numeric(0.02),
    N4 = as.numeric(0.02),
    C1 = as.numeric(0.02),
    C2 = as.numeric(0.02),
    C3 = as.numeric(0.02),
    C4 = as.numeric(0.02),
    C5 = as.numeric(0.02),
    M1 = as.numeric(0.02),
    M2 = as.numeric(0.02))

    rownames(plot.df) <- "TP53"

    psm.df <- data.frame(Protein = "TP53",
    PSMs.for.quant = as.numeric(31))

    rownames(psm.df) <- "TP53"

    proteinPlot <- plotBarcode(plot.df, "TP53", psm.df)
    }

[Package SubCellBarCode version 1.6.0 Index]