plot.sPLSDA.scatter.123

Combines the component1-vs-component2 and component3-vs-component2 scatters of a sPLS-DA.

plot.sPLSDA.scatter.123(
  DEprot.sPLSDA.object,
  color.column = NULL,
  shape.column = NULL,
  label.column = NULL,
  dot.colors = NULL,
  ellipse = TRUE,
  ellipse.level = 0.95,
  title = NULL
)

Arguments

DEprot.sPLSDA.object

An object of class DEprot.sPLSDA.

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).

dot.colors

Color-vector to use for the points. Default: NULL (automatic colors).

ellipse

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

ellipse.level

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

title

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

Value

A patchwork object.

See also

perform.sPLSDA, plot.sPLSDA.scatter

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.scatter.123(DEprot.sPLSDA.object = splsda,
                        shape.column = "replicate")
#> Warning: The following aesthetics were dropped during statistical transformation: shape.
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?
#> Warning: The following aesthetics were dropped during statistical transformation: shape.
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?