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kevinblighe / EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling
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output graph doesn't display any of the selected genes #111

Open ofleitas opened 1 year ago

ofleitas commented 1 year ago

Hello

I am trying to highlight some genes in the volcano plot. However, the output graph doesn't display any of the selected genes.

This is the code:

p <- EnhancedVolcano(X, lab = row.names(X), x = 'log2FC', y = 'padj',title = 'Control treated vs Resistant treated', pCutoff = 1e-02, FCcutoff = 1, pointSize = 3, labSize = 3, colAlpha = 1, cutoffLineType = 'dashed', cutoffLineWidth = 0.8, legendLabels = c('NS','Log2FC','padj','padj & Log2FC'), gridlines.major = FALSE, gridlines.minor = FALSE, legendPosition = 'right', legendLabSize = 16, legendIconSize = 5, subtitle = NULL, drawConnectors = TRUE, widthConnectors = 0.75, boxedLabels = TRUE,max.overlap = 25, selectLab = c("csbX","rfbD","rffG","phoP","dcd","aphA","mdtB","galF","sotB"))

hmlopezbertoni commented 1 year ago

I'm having the same issue, were you able to find a solution?

ofleitas commented 1 year ago

Hello

I replaced lab = rownames(X) by lab=X$gene_ID, that worked for me.

On Sat, Apr 8, 2023 at 12:04 PM hmlopezbertoni @.***> wrote:

I'm having the same issue, were you able to find a solution?

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