plot.sPLSDA.biplot

Overlays the loadings of the selected proteins on the scatter of two components of a sPLS-DA.

plot.sPLSDA.biplot(
  DEprot.sPLSDA.object,
  comp.x = 1,
  comp.y = 2,
  color.column = NULL,
  shape.column = NULL,
  label.column = NULL,
  ellipse = FALSE,
  ellipse.level = 0.95,
  plot.zero.line.x = TRUE,
  plot.zero.line.y = TRUE,
  n.loadings = 10,
  loading.color = "turquoise4",
  loading.arrow.size = 0.6,
  loading.label.size = 3,
  loading.alpha = 0.7,
  loading.scale = 0.8
)

Arguments

DEprot.sPLSDA.object

An object of class DEprot.sPLSDA.

comp.x

Number indicating which component to display on the x-axis. Default: 1.

comp.y

Number indicating which component to display on the y-axis. Default: 2.

color.column

String indicating the name of the column in the metadata to use as factor for the dot colors. Default: NULL (the column used to fit the model).

shape.column

String indicating the name of the column in the metadata to use as factor for the dot shapes. Default: NULL (all dots).

label.column

String indicating the name of the column in the metadata to use as label of the dots. Default: NULL (no labeling).

ellipse

Logical value indicating whether a confidence ellipse should be drawn around each group. Default: FALSE.

ellipse.level

Numeric value (0-1) indicating the confidence level of the ellipses. Default: 0.95.

plot.zero.line.x

Logical value to indicate whether to plot a gray dashed line in correspondence of x=0. Default: TRUE.

plot.zero.line.y

Logical value to indicate whether to plot a gray dashed line in correspondence of y=0. Default: TRUE.

n.loadings

Number of proteins to display, ranked by their distance from the origin in the plane displayed. Default: 10.

loading.color

String indicating the color of the arrows and of their labels. Default: "turquoise4".

loading.arrow.size

Numeric value indicating the linewidth of the arrows. Default: 0.6.

loading.label.size

Numeric value indicating the font size of the labels. Default: 3.

loading.alpha

Numeric value (0-1) indicating the transparency of arrows and labels. Default: 0.7.

loading.scale

Numeric multiplier to manually adjust the length of the arrows. Default: 0.8.

Value

A ggplot object.

Details

Only the proteins retained on at least one of the two components displayed can appear: a protein dropped by the sparsity penalty has a coefficient of exactly zero and no direction to point to.

See also

perform.sPLSDA, plot.sPLSDA.scatter, plot.sPLSDA.loadings

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.biplot(DEprot.sPLSDA.object = splsda,
                   comp.x = 1,
                   comp.y = 2,
                   n.loadings = 5)