methylation-foo/Volcano Plot at main · Jones-Lab-CSMC/methylation-foo · GitHub

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library(TCGAbiolinks)

TCGAVisualize_volcano(results$MethylationDifference, results$rawpvalue,
                      filename = "",
                      ylab = "Raw P-Values",
                      xlab = "Methylation Difference",
                      #title = "Treated vs Untreated, outlier excluded",
                      legend = "Sample",
                      label = c("Not Significant", "Hypermethylated", "Hypomethylated"),
                      xlim = NULL,
                      ylim = NULL,
                      color = c("black", "orange", "blue"),
                      names = rownames(ret),
                      names.fill = FALSE,
                      show.names = "significant",
                      x.cut = 0.1,
                      y.cut = 0.0005,
                      height = 5,
                      width = 10,
                      #highlight = CellCycleProbes_3_6_17$G1b ,
                      highlight.color = "red",
                      names.size = 0,
                      dpi = 300)