Ann Loraine added a comment - 19/Dec/23 12:44 PM Re-running the .Rmd files did not change results files, just the knitted Markdown. The .Rmd files include a call to the system "date" function, updating the header of the knitted output PDF file to show the current date. All looks good. Proceeding to merge PR from Molly Davis.

Ann Loraine added a comment - 19/Dec/23 12:28 PM - edited Files changed include: commit cd485e7d2b06be5622954609647eac170df32402 (HEAD -> IGBF-3529, molly/IGBF-3529) Author: MollyDSnk <MollyDSnk@users.noreply.github.com> Date: Fri Dec 15 11:09:19 2023 -0500 IGBF-3529 Change Volcano plot colors & X-axis - - 72_F3H_PollenTube/CustomVolcanoPlots-SL4-DeSeq2.pdf - - 72_F3H_PollenTube/FindControlVsStressDEGenes-SL4-DESeq2.pdf - - 72_F3H_PollenTube/FindControlVsStressDEGenes-SL4-edgeR.pdf - - 72_F3H_PollenTube/FindControlVsStressDEGenes-SL5-DESeq2.pdf - - 72_F3H_PollenTube/FindControlVsStressDEGenes-SL5-edgeR.pdf 6 6 72_F3H_PollenTube/MakeCustomVolcanoPlots.Rmd - - 72_F3H_PollenTube/MakeCustomVolcanoPlots.pdf 7 7 72_F3H_PollenTube/StatFunctions.R commit 92a394323efb071ef8a881f0f5780d5b38e1ba32 (origin/main, origin/HEAD, molly/main, main) Author: aloraine <aloraine@uncc.edu> Date: Wed Nov 22 15:00:04 2023 -0500 IGBF-3504 Group1 should be numerator, group2 denominator 7 6 72_F3H_PollenTube/FindMutantVsWildtypeDEGenes-DESeq2.Rmd - - 72_F3H_PollenTube/FindMutantVsWildtypeDEGenes-DESeq2.pdf 101943 103055 72_F3H_PollenTube/results/MvW-SL4.txt 99086 97656 72_F3H_PollenTube/results/MvW-SL5.txt Molly has changed the PDFs resulting from running differential expression analysis, reflecting the change in plotting function present in StatFunction.R, in which the point colors were changed, as noted above. Checking to see if the results file itself changes upon re-running the corresponding .Rmd files.

Ann Loraine added a comment - 19/Dec/23 12:21 PM Pulling branch to my local for review.

Molly Davis added a comment - 15/Dec/23 11:16 AM - edited Reviewer : Pull each file from the branch and make sure that the colors are a more vibrant blue and red and that the x-axis min and max are (-10,10). Make sure no other code was changed and that the volcano plots are visually appealing. Do the plots need larger points? Are the colors vibrant enough? Are the point shapes appropriate on the plots? Thank you! Robert Reid If everything is fine, here is the Pull Request so things can move forward while I am on holiday break! https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/38

Molly Davis added a comment - 15/Dec/23 11:11 AM - edited Branch : https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3529 Changes : The only things that were changed to the code was the volcano plots colors and the x-axis min and max to (-10,10). The code changes the knitted pdf files because the volcano plots not have different colors and x-axis.