Higlight a dot in a volcano plot using EnhancedVolcano

Question

[santiagoboccardo31]

Hi, I have been using enhanced volcano tool to construct a volcano plot of DEGs between two conditions. I could construct the volcano plot and label and color in red particular genes related to a specific biological pathway. However, some of the colored dots are covered by uncolored (gray) dots corresponding to non-related genes with a similar expression, as you can see in the next image:

The script I've made is the following:

I need the gray dots to stop covering the red-labeled ones. I other words, I need the red dots to be in the front of the image. Can anyone tell me how to do that?

[ATpoint]

The easiest is probably to save the plot object to a variable such as p <- EnhancedVolcano(...) and then modify the order of p$data. As the order of the points being plotted is determined by the order in p$data it is probably enough to do:

library(dplyr)

p$data <- p$data %>% arrange(GeneName)

and then without anything else plot it again by just typing p. Maybe it is arrange(-GeneName), I cannot test as you do not provide reproducible data or copy/paste-ready code ;-)

[GenoMax]

santiagoboccardo31 : It would be better if you can actually copy and paste the code in (User 101010 button in edit window to format the text) instead of screenshot above. You can edit the original post and make the change.

[santiagoboccardo31]

Thank you very much! I will try that :)

[GenoMax]

High-light then entire section you want to designate as code and then click on 101010 button. You may or may not see a preview so go ahead complete the edit.

[santiagoboccardo31]

Thank you very much! I will do that next time :D

[santiagoboccardo31]

Yes, definitely! I tried to do that but it only transformed the first line of my code to the 101010 format and I don't find the way to get the full code in 101010 format. That's why I pasted the code as an Image :s Sorry for that!