Molly Davis added a comment - 29/Jan/24 3:09 PM 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

Molly Davis added a comment - 29/Jan/24 3:11 PM - edited 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.

Robert Reid added a comment - 31/Jan/24 4:01 PM 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

Molly Davis added a comment - 01/Feb/24 2:53 PM - edited Final Draft : Hi all , I hope everyone had a wonderful holiday season! As a reminder we wanted to add a ceiling to the the volcano plots to present a more volcano shaped plot. To do this we added a ceiling that ensures no points are lost and are just kept at the ceiling if higher than 20 -log10 P. 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 Needs a final review!

Robert Reid added a comment - 02/Feb/24 9:16 AM Yes !! This looks great, send it off and move this task to done !!