contrast.scatter — contrast.scatter • DEprot

Plots a scatter plot of the log2(fold change expression) derived from two differential analyses contrasts.

contrast.scatter(
  DEprot.analyses.object,
  contrast.x,
  contrast.y,
  regression.line.color = "firebrick",
  correlation.method = "pearson",
  add.foldchange.threshold = TRUE,
  symmetric.axes = TRUE
)

Arguments

DEprot.analyses.object: An object of class DEprot.analyses.
contrast.x: Integer indicating the position of the contrast to use for the x-axis of the plot.
contrast.y: Integer indicating the position of the contrast to use for the y-axis of the plot.
regression.line.color: String indicating any R-supported color to use for the regression line and error. Default: "firebrick".
correlation.method: String indicating the clustering method to use to generate the correlation matrix. Possible options: 'pearson', 'spearman', 'kendall'. Default: "pearson".
add.foldchange.threshold: Logical value to indicate whether two gray rectangles should be used to highlight the non-differential area in the plot, based on the foldchange threshold indicated during the differential analyses. Default: TRUE.
symmetric.axes: Logical value indicating whether the axes should be forces to be symmetric between x and y. Default: TRUE.

Value

A scatter plot of class ggplot2.