showing the name of top 20 differentially genes in EnhancedVolcano

Question

[momo.bhmd]

hi I'm biologist and I have a very primitive knlowdge in R. Recently, I found this amazing tool "EnhancedVolcano" to visualize the DEG between two different cells type. I want to show the name of only the top 20 differentially expressed genes in the both side of the volcano plot, do you have any recommendation ? Thanks a lot

Answer 1

[GenoMax]

Have you looked at the vignette?

Also: A: How to just add some selected gene names to a volcano plot

[momo.bhmd]

yes but it was not reported :-(

[Kevin Blighe]

Hey, my colleagues and I developed this tool. You would have to find out the top 20 and then pass these gene names as a vector to the selectLab parameter. This should work.

To get the top 20 on both sides of the plot, you could do this manually by looking at the results table, or programmatically via head(), subset(), or some other function for subsetting.

In your plot, I would also increase those label sizes. Make use of the full plot window and don't be shy about using up white-space.

[momo.bhmd]

Thanks a lot Kevin for your help :-)

[momo.bhmd]

Hi kevin, in the same context, I want to highlight a specific set of genes with different colour without overriding the existing colour of the Volcano plot (colouring only a specific set of genes while keeping the default colour of the volcano plot) .. I tried ColCustom parameter but it’s not working. D you have any suggestion ? thanks a lot :-)

[Kevin Blighe]

For that part, there are sections in the vignette. Did you follow them, or, what happened ... ? please share your code and the output of your colCustom variable, if possible.

[momo.bhmd]

Thanks again for your time :-) I want the highlight the genes "ISG" in 'gold' while keeping the standard theme of the EnhancedVolcano. Also, I want to hide the transcript name. I apologize for asking many questions, my coding knowledge are more than basic. Here's my code

keyvals.shape <- ifelse(
  res1$ID %in% i, 'gold',
  'black')
keyvals.shape[is.na(keyvals.shape)] <- 'black'
names(keyvals.shape)[keyvals.shape == 'black'] <- 'Others'
names(keyvals.shape)[keyvals.shape == 'gold'] <- 'ISG'
EnhancedVolcano(res1,
                lab = rownames(res1),
                x = "logFC",
                y = 'adj.P.Val',
                title = NULL,
                subtitle = "mTEC vs SkinEC",
                pCutoff = 0.01,
                FCcutoff = 1,
                labSize = 2.4,
                colAlpha = 1,
                pointSize = 1,
                caption = NULL,
                selectLab = NULL,
                colCustom = keyvals.shape,
                col = c('grey30', 'forestgreen', 'royalblue', 'red2'))

'i' contain the list of the genes that I want to highlight

[Kevin Blighe]

To hide the labels, I think that it is just lab = NULL or lab = NA.

Also, I can see that the colCustom is actually functioning; however, the issue is that the ISG genes are mostly concealed behind others. The only current way to get around this is to re-order your input results table, res1, so that the ISG genes are at the bottom of res1, meaning that they will be plot last and will be more prominent in the plot space.

[momo.bhmd]

Thanks a lot and the other issue that I was not able to keep the standard colour the EnhancedVolcano col = c('grey30', 'forestgreen', 'royalblue', 'red2'), do you have any suggestion ?