We would like to add a feature to our volcanoPLots function so that there is an optional argument to specify the Y-axis ceiling.

The user would pass a variable for the Y-axis when they call the function.

Currently it looks like this:
volcano_plot<- function(d, title, method="DESeq2",Q=0.05) {
...

The method would look like this:
volcano_plot<- function(d, title, method="DESeq2",Q=0.05,yaxis=NULL) {
....

Or this is VERY close to what might work:

volcano_plot<- function(d, title, method="DESeq2",Q=0.05,yaxis) {
colorBlindGrey8 <- c("#999999", "#E69F00", "#56B4E9", "#009E73",
"#F0E442", "#0072B2", "#D55E00", "#CC79A7")
if (method=="DESeq2") {
lfc_colname = "log2FoldChange"
padj_colname = "padj"
p_colname = "pvalue"

• if (!is.null(yaxis)) { d$pvalue= ifelse(-log10(d$pvalue) < yaxis,d$pvalue,yaxis) }

  *
  }
  if (method=="edgeR")

  Unknown macro: { lfc_colname = "logFC" padj_colname = "Q" p_colname = "PValue" *if (!is.null(yaxis)) { d$Pvalue= ifelse(-log10(d$Pvalue) < yaxis,d$Pvalue,yaxis) }* }

  pCutoffCol = padj_colname

Not tested yet.