pcaPlot {qPLEXanalyzer} | R Documentation

## PCA plot

### Description

PCA plots of the samples within MSnset

### Usage

    pcaPlot(
      MSnSetObj,
      omitIgG = FALSE,
      sampleColours = NULL,
      transFunc = log2xplus1,
      transform = TRUE,
      colourBy = "SampleGroup",
      title = "",
      labelColumn = "BioRep",
      labelsize = 4,
      pointsize = 4,
      x.nudge = 4,
      x.PC = 1
    )

### Arguments

`MSnSetObj` | MSnSet; an object of class MSnSet
`omitIgG` | Logical: whether to remove IgG from the PCA plot
`sampleColours` | character: A named vector of colours for samples
`transFunc` | func: internal helper function for log transformation
`transform` | logical: whether to log transform intensities
`colourBy` | character: column name to use for colouring samples from `pData(MSnSetObj)`
`title` | character: title for the plot
`labelColumn` | character: column name from `pData(MSnSetObj)` to use for labelling points on the plot
`labelsize` | numeric: size of the labels
`pointsize` | numeric: size of plotting points
`x.nudge` | numeric: distance to move labels along the x-axis away from the plotting points
`x.PC` | numeric: The principle component to plot on the x-axis; the following PC will be plotted on the y-axis

### 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)
    exprs(MSnSet_data) <- exprs(MSnSet_data)+0.01
    pcaPlot(MSnSet_data, omitIgG = TRUE, labelColumn = "BioRep")

    # custom colours and PC2 v PC3
    customCols <- rainbow(length(unique(pData(MSnSet_data)$SampleGroup)))
    names(customCols) <- unique(pData(MSnSet_data)$SampleGroup)
    pcaPlot(MSnSet_data,
            omitIgG = TRUE,
            labelColumn = "BioRep",
            sampleColours = customCols,
            x.PC=2)

[Package qPLEXanalyzer version 1.8.2 Index]