Hi all,

I hope everyone had a wonderful holiday season!

Dr. Reid and I have finished working on the ceiling code for the volcano plots and wanted to send out an update. We made the y-axis max 20 on the volcano plots and any points that had a value higher than 20 were edited to hit the ceiling of the plot. The updated files are the following in the repo:

• Plots: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/CustomVolcanoPlots-SL4-DeSeq2.pdf
• Knitted markdown: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/MakeCustomVolcanoPlots.pdf
• Code: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/MakeCustomVolcanoPlots.Rmd

If interested, the line of code that made this possible was d$pvalue= ifelse(-log10(d$pvalue) < 20,d$pvalue,1e-20).

Let us know what you think and if you have any more requests! We were thinking of making the points at the ceiling a different color and/or shape and then making sure there was no overlapping issues for the points.

Thanks so much!

Sincerely, Molly

Question: Should I add an explanation of why we wanted to create a ceiling in the first place? If so, please add your thoughts on why we need a ceiling for the volcano plots.

These links look good.

The email reads well and is straightforward.

To answer your question, yes. Let's tell them why we were adding the ceiling. Something to the effect of:

"As a reminder we wanted to add a ceiling to the our volcano plots so that we don't lose any data points when we present a zoomed in volcano plot. And to ensure that the volcano plot still retains its appearance of a volcano, demonstrating the expected distribution of data points."

Something weird is happening in Jira related to moving the task in the columns.

So I am just assigning this task back to Molly.

R

Final Draft:

Needs a final review!

Yes !! This looks great, send it off and move this task to done !!