plot.PC.scatter

Source: R/plot.PC.scatter.R

Plot a scatter of the PCs from an object generated by perform.PCA.

# S3 method for class 'PC.scatter'
plot(
  DEprot.PCA.object,
  PC.x = 2,
  PC.y = 1,
  color.column = "column.id",
  shape.column = NULL,
  label.column = NULL,
  plot.zero.lines = TRUE
)

Arguments

DEprot.PCA.object

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

PC.x

Number indicating which Principal Component (PC) display on the x-axis. Default: 2 (PC2).

PC.y

Number indicating which Principal Component (PC) display on the y-axis. Default: 1 (PC1).

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).

plot.zero.lines

Logical value to indicate whether to plot two gray dashed lines in correspondence of y=0 and x=0. Default: TRUE.

Value

A ggplot object.

See also

perform.PCA

Author

Sebastian Gregoricchio

Examples

# Perform Principal Component Analyses (PCA)
pca <- perform.PCA(DEprot.object = DEprot::test.toolbox$dpo.imp)

# Plot PC1-vs-PC2 scatter
plot.PC.scatter(DEprot.PCA.object = pca,
                color.column = "condition",
                shape.column = "replicate",
                label.column = "replicate")


# Plot PC2-vs-PC3 scatter
plot.PC.scatter(DEprot.PCA.object = pca,
                PC.x = 3,
                PC.y = 2,
                color.column = "condition",
                shape.column = "replicate",
                label.column = "replicate")