The new versions of the volcano plots impose a y-axis maximum value on all points shown. That is, if a point has a y-value that is larger than a set maximum values, we draw those points with y-values equal to that ceiling - currently set to 20 (this is negative log value).

See: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/CustomVolcanoPlots-SL4-DeSeq2.pdf

However, there are so many of these points that they overlap and it's hard to see how many there are. Also, it isn't entirely clear which points got crushed and which did not. It is also not clear from looking at the plot that this is happening.

Our idea is to address by making changes to how the "crushed" ceiling points look.

Some proposed options:

• Changing their shape and/or shape. These are proposed solutions to the problem of having misleading point positions. By making the "ceiling points" look different, we might make it more obvious to readers that their apparent y-values are not their actual y-values.
• Imposing some type of jittering in y-axis dimension above and below the ceiling threshold. This is proposed solution for the problem of not being able to tell how many points got "crushed".