Y-axis break in Volcano Plot

Question

[rajdeepboral00]

res_lumbar <-read.csv("res_lumbar_results_new.csv",header=TRUE)

sig_lumbar<- subset(res_lumbar, padj < 0.1 & abs(log2FoldChange) >= 1)

up_lumbar <- subset(sig_lumbar, log2FoldChange >= 1)

down_lumbar<- subset(sig_lumbar, log2FoldChange <= -1)

cat("Lumbar Upregulated:", nrow(up_lumbar), "\n")

cat("Lumbar  Downregulated:", nrow(down_lumbar), "\n")

EnhancedVolcano(res_lumbar,
                lab = NA,
                x = "log2FoldChange",
                y = "padj",
                title = "Volcano Plot: Thoracic CT vs IT",
                xlab = "Log2 Fold Change",
                ylab = "-log10(p-value)",
                pCutoff = 0.05,
                FCcutoff = 1,
                pointSize = 1,
                colAlpha = 0.75,
                legendPosition = "right",
                legendLabSize = 12,
                legendIconSize = 4,
                drawConnectors = FALSE,
                ylim=c(0,130)
)

This is the code i have used. While plotting the Volcano plots, due to few outliers, my whole plot is getting skewed, can anyone please suggest me how to include nreaks in the y-axis. Any help is appreciated

[GenoMax]

Any help is appreciated

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[antonioggsousa]

I am not familiar with the package EnhancedVolcano, but based on your code, should not you be able to change the y-axis limits through the argument ylim in the function EnhancedVolcano()? As it is, the y-axis will be ranging from 0 to 130. Did you try to change ylim=c(0,130) to ylim=c(0,100), or whatever range you want to see represented in the y-axis scale?