plot.PC.scatter.123

Source: R/plot.PC.scatter.123.R

Plot combined scatter of the PCs 1-2,2-3 from an object generated by perform.PCA.

# S3 method for class 'PC.scatter.123'
plot(
  DEprot.PCA.object,
  color.column = "column.id",
  shape.column = NULL,
  label.column = NULL,
  dot.colors = NULL,
  plot.zero.line.y.12 = TRUE,
  plot.zero.line.x.12 = TRUE,
  plot.zero.line.y.23 = TRUE,
  plot.zero.line.x.23 = TRUE
)

Arguments

DEprot.PCA.object

An object of class DEprot.PCA.object, as generated by perform.PCA.

color.column

String indicating the name of the column in the metadata to use as factor for the dot colors. Default: "column.id" (each sample a color).

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 indicating the colors to use for the points in the plot. If NULL (default) or the number of colors is lower than the required, automatic colors will be assign using the rainbow function. Default: NULL.

plot.zero.line.y.12

Logical value to indicate whether to plot two gray dashed lines in correspondence of y=0 in the PC1-vs-PC2 plot. Default: TRUE.

plot.zero.line.x.12

Logical value to indicate whether to plot two gray dashed lines in correspondence of x=0 in the PC1-vs-PC2 plot. Default: TRUE.

plot.zero.line.y.23

Logical value to indicate whether to plot two gray dashed lines in correspondence of y=0 in the PC2-vs-PC3 plot. Default: TRUE.

plot.zero.line.x.23

Logical value to indicate whether to plot two gray dashed lines in correspondence of x=0 in the PC2-vs-PC3 plot. Default: TRUE.

Value

A patchwork object result of a combination of two ggplot objects.