compare.ranking — compare.ranking • DEprot

Compare the two possible methods for the gene ranking used to perform Gene Set Enrichment Analyses (GSEA).

compare.ranking(
  DEprot.analyses.object,
  contrast,
  color.up = "indianred",
  color.down = "steelblue",
  regression.line.color = "purple"
)

Arguments

DEprot.analyses.object: An object of class DEprot.analyses.
contrast: Number indicating the position of the contrast to use for the plotting.
color.up: String indicating any R-supported color that will be used for dots with a positive fold change. Default: "indianred".
color.down: String indicating any R-supported color that will be used for dots with a negative fold change. Default: "steelblue".
regression.line.color: String indicating any R-supported color to use for the regression line and error. Default: "purple".

Two ggplots combined in an object of class patchwork.

if (FALSE) { # \dontrun{
  ranking <- compare.ranking(DEprot::test.toolbox$diff.exp.limma, contrast = 1)
  ranking
} # }