plot.perf.pls {mixOmics} | R Documentation

## Plot for model performance for PLS analyses

### Description

Function to plot performance criteria, such as MSEP, RMSEP, R^2, Q^2 for s/PLS methods as a function of the number of components.

### Usage

    ## S3 method for class 'perf.pls.mthd'
    plot(
      x,
      criterion = "MSEP",
      xlab = "Number of components",
      ylab = NULL,
      LimQ2 = 0.0975,
      LimQ2.col = "grey30",
      sd = NULL,
      pch = 1,
      pch.size = 3,
      cex = 1.2,
      col = color.mixo(1),
      title = NULL,
      ...
    )

    ## S3 method for class 'perf.spls.mthd'
    plot(
      x,
      criterion = "MSEP",
      xlab = "Number of components",
      ylab = NULL,
      LimQ2 = 0.0975,
      LimQ2.col = "grey30",
      sd = NULL,
      pch = 1,
      pch.size = 3,
      cex = 1.2,
      col = color.mixo(1),
      title = NULL,
      ...
    )

### Arguments

`x` | an `perf.pls` object.
`criterion` | character string. What type of validation criterion to plot for `pls` or `spls`. One of `"MSEP"`, `"RMSEP"`, `"R2"` or `"Q2"`. More measures available for pls2 methods. See `perf`.
`xlab, ylab` | titles for x and y axes. Typically character strings, but can be expressions (e.g., `expression(R^2)`).
`LimQ2` | numeric value. Signification limit for the components in the model. Default is `LimQ2 = 0.0975`.
`LimQ2.col` | character string specifying the color for the `LimQ2` line to be plotted. If `"none"` the line will not be plotted.
`sd` | If 'nrepeat' was used in the call to 'perf', error bar shows the standard deviation if sd=TRUE. For mint objects sd is set to FALSE as the number of repeats is 1.
`pch` | Plot character to use.
`pch.size` | Plot character size to use.
`cex` | A numeric which adjusts the font size in the plot.
`col` | Character. Colour to be used for data points.
`title` | Character, Plot title. Not used by PLS2 feature-wise measure plots.
`...` | Not used.

### Details

`plot.perf` creates one plot for each response variable in the model, laid out in a multi-panel display. See ?perf for examples.

### Value

none

### Author(s)

Al J Abadi

### References

Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics feature selection and multiple data integration. PLoS Comput Biol 13(11): e1005752

### See Also

`pls`, `spls`, `plsda`, `splsda`, `perf`.

[Package mixOmics version 6.16.3 Index]