plot.perf.pls: Plot for model performance for PLS analyses

plot.perf.plsR 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, LĂȘ 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.


mixOmicsTeam/mixOmics documentation built on Nov. 4, 2024, 8:56 a.m.