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 object created by `ggplot`

### 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 1.10.0 Index]