rliPlot {qPLEXanalyzer} | R Documentation

## Relative log intensity plot

### Description

Relative log intensity (RLI) plots of the samples within MSnset

### Usage

    rliPlot(
      MSnSetObj,
      title = "",
      sampleColours = NULL,
      colourBy = "SampleGroup",
      omitIgG = TRUE
    )

### Arguments

`MSnSetObj` | MSnSet; an object of class MSnSet
`title` | character: title for the plot
`sampleColours` | character: a named vector of colours for samples
`colourBy` | character: column name to use for colouring samples from pData(MSnSetObj)
`omitIgG` | logical: whether to remove IgG from the RLI plot

### Details

An RLI-plot is a boxplot that can be used to visualise unwanted variation in a data set. It is similar to the relative log expression plot developed for microarray analysis - see Gandolfo and Speed (2018). Rather than examining gene expression, the RLI plot uses the MS intensities for each peptide or the summarised protein intensities.

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`

### References

Gandolfo LC, Speed TP (2018) RLE plots: Visualizing unwanted variation in high dimensional data. PLoS ONE 13(2): e0191629. https://doi.org/10.1371/journal.pone.0191629

### 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)
    rliPlot(MSnSet_data, title = "qPLEX_RIME_ER")

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

[Package qPLEXanalyzer version 1.10.0 Index]