plot.sPLSDA.loadings

Plots the loadings of the proteins retained on a component of a sPLS-DA, colored by the class in which each of them is the highest.

plot.sPLSDA.loadings(
  DEprot.sPLSDA.object,
  component = 1,
  n.proteins = 25,
  group.colors = NULL,
  protein.names.pattern = NULL,
  bar.width = 0.75,
  axes.text.size = 9,
  title = NULL
)

Arguments

DEprot.sPLSDA.object

An object of class DEprot.sPLSDA.

component

Numeric value indicating the component to display. Default: 1.

n.proteins

Numeric value indicating the maximum number of proteins to display, ranked by absolute loading. Default: 25.

group.colors

Color-vector (optionally named on the classes) used for the bars. Default: NULL (automatic colors).

protein.names.pattern

String indicating a pattern to be passed to gsub and removed from the protein names. Default: NULL (no changes).

bar.width

Numeric value indicating the width of the bars. Default: 0.75.

axes.text.size

Numeric value indicating the font size of the axis text. Default: 9.

title

String indicating the title of the plot (markdown annotation supported). Default: NULL (automatic title).

Value

A ggplot object.

Details

The sign of a loading is only interpretable once the orientation of the component is fixed, which perform.sPLSDA does through the reference.group argument: a positive coefficient marks a protein pulling the samples towards that group. The color adds the information the coefficient alone does not carry, namely in which class the protein is actually the most abundant, assigned by the highest median as done by mixOmics::plotLoadings.

See also

perform.sPLSDA, plot.sPLSDA.stability, get.sPLSDA.results

Author

Sebastian Gregoricchio

Examples

splsda <- perform.sPLSDA(DEprot.object = DEprot::test.toolbox$dpo.imp,
                         group.column = "condition",
                         keepX = 5,
                         validate = FALSE)
#> Warning: The number of 'folds' (5) is larger than the smallest class (4 samples): 'folds' has been set to 4.

plot.sPLSDA.loadings(DEprot.sPLSDA.object = splsda,
                     component = 1,
                     n.proteins = 5)