I have recently found myself making multiple heatmaps for visualization of differential gene expression results between replicates in two experimental conditions.
The default settings in the plotting software I use color:
- Upregulated genes --> red
- Downregulated genes --> green
- Unchanged genes --> black
My intuition screams at me that this color scheme is reversed, and that upregulated genes should be green and that downregulated genes should be red. I have asked several labmates about their intuition regarding this color scheme, and have found about a 50/50 split in those that intuitively agree with each different scheme.
In my searching on this topic, I have found that several programs plot heatmaps with the same default colors as the program I'm using (red=upregulated, green=downregulated). Additionally, I have been told in conversation that this is essentially an accepted standard.
If this is indeed the convention, I will begin trying to rewire my intuition, but I want to confirm that it is before I do so. However I have not yet been able to find any "official" guidelines from agencies, publishers, authorities in the field, etc., specifying the use of red/green in heatmaps.
I do know that there are many suggestions for alternative heatmap color schemes, but I'm interested in finding an official answer for the red/green scheme specifically.
Edit: Several comments have stated that there is no such standard as described above. Therefore I am modifying the following question somewhat to:
Are there "official" guidelines from agencies, publishers, authorities in the field, etc., specifying the use of red/green in heatmaps? Or conversely are there any “official” guidelines stating that there is no such specification and/or that any such selection of colors is acceptable?