volcanoplots with different colors for up/down regulated genes

Question

[adR]

Hi,

I would appreciate it if anyone could direct me on how to give different colors for the up and down-regulated genes using the R Bioconductor package enhancedvolcano.

Just as indicated in the following link.

Thanks!

https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html#:~:text=A%20volcano%20plot%20is%20a,the%20most%20biologically%20significant%20genes.

Answer 1

[Kevin Blighe]

Hey,

This can be achieved via customised coding or EnhancedVolcano. Please take a look at the vignette, where there is a dedicated section for this (see Section 4.9): http://bioconductor.org/packages/devel/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html

Kevin

[adR]

Thank you so much! However, when I am changing the labels(high, low, mid) by my keywords, let say "up," "down," and "none," those genes pop up in the plot are not coming just the dot points. AD

[Kevin Blighe]

To receive help, you will have to share the code that you are running, and [preferably] a fully reproducible sample dataset. Thanks.

[adR]

I got my mistake... Thanks! Now it is solved!