Hi,
I am trying to make a volcano plot, when I enter this, the plot for log2foldchange (y axis) is maxed at 300. Therefore I would like to increase its limit.
` res_wBE_muc <- results(dds, contrast=c("condition", "OAC_wBE","Normal_Muc"))
EnhancedVolcano(res_wBE_muc, lab = rownames(res_wBE_muc), x = 'log2FoldChange', y = 'pvalue', title = 'Volcano Plot of OACwBE vs Mucosa', pCutoff = 0.05, FCcutoff = 1, pointSize = 3.0, labSize = 6.0)
`
Then, I tried inputting this in:
EnhancedVolcano(res_wBE_muc, lab = rownames(res_wBE_muc),
x = 'log2FoldChange',
y = 'pvalue',
ylim = c(0, max(-log10(res_wBE_muc[["padj"]]), na.rm = TRUE) + 5),
title = 'Volcano Plot of OACwBE vs Mucosa',
pCutoff = 0.05,
FCcutoff = 1,
pointSize = 3.0,
labSize = 6.0)
But it returned with an error message and no volcano plot was shown.
I tried to change its y maximum limit to more than 300 (e.g. 301), it will still show the same error.
2: Position guide is perpendicular to the intended axis. Did you mean to specify a different guide position?
May I request your assistance to understand where the problem is? Thank you
