intensityPlot {qPLEXanalyzer} | R Documentation

## Intensity Distribution Plot

### Description

Intensity distribution plot of all the samples

### Usage

    intensityPlot(MSnSetObj, sampleColours=NULL, title="", colourBy="SampleGroup",
                              transform=TRUE, xlab="log2(intensity)",
                              trFunc=log2xplus1)

### Arguments

`MSnSetObj` | MSnSet; an object of class MSnSet
`sampleColours` | character: a vector of colors for samples
`title` | character: title for the plot
`colourBy` | character: column name from pData(MSnSetObj) to use for coloring samples
`transform` | logical: whether to log transform intensities
`xlab` | character: label for x-axis
`trFunc` | func: internal helper function for log transformation

### Details

The column provided to the "colourBy" argument will be used to colour the samples. The colours will be determined using the function assignColours, alternatively the user may specify a named vector of colours using the "sampleColours" argument. The names of the "sampleColours" vector should match the unique values in the "colourBy" column.

### Value

An intensity distribution plot for quantitative proteomics data.

### Examples

    data(human_anno)
    data(exp3_OHT_ESR1)
    MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, metadata=exp3_OHT_ESR1$metadata_qPLEX1,
    indExpData=c(7:16), Sequences=2, Accessions=6)
    intensityPlot(MSnSet_data, title = "qPLEX_RIME_ER")

    # custom colours
    customCols <- rainbow(length(unique(pData(MSnSet_data)$SampleGroup)))
    names(customCols) <- unique(pData(MSnSet_data)$SampleGroup)
    intensityPlot(MSnSet_data, title = "qPLEX_RIME_ER", sampleColours = customCols)

[Package qPLEXanalyzer version 1.5.0 Index]