plot.sPLSDA.cumulative

Source: R/sPLS.DA_plots.R

Plots the proportion of protein variance carried by each component of a sPLS-DA, with the cumulative curve on top.

plot.sPLSDA.cumulative(
  DEprot.sPLSDA.object,
  bar.color = "steelblue",
  line.color = "navyblue",
  title = NULL
)

Arguments

DEprot.sPLSDA.object

An object of class DEprot.sPLSDA.

bar.color

String indicating the color to use for the bar fill. Default: "steelblue".

line.color

String indicating the color to use for the line and the dots of the cumulative curve. Default: "navyblue".

title

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

Value

A ggplot object.

Details

A sPLS-DA component is built to separate the classes, not to capture variance, and it only sees the handful of proteins retained by keepX. The percentages are therefore much lower than the ones of a PCA computed on the same data, and comparing the two is meaningless: what this plot shows is how the (little) variance used by the model is spread over the components.

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.cumulative(DEprot.sPLSDA.object = splsda)