Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.5
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Sprint:Fall 8
Description
During a meeting Muday lab requested to change the volcano plot colors to a more saturated blue and red. Then the middle would be grey instead of black. They also requested to have all of the x-axis (-10,10) including the custom volcano plots.
Note: These changes need to be implemented with all of the other FindControlVsStress & MakeCustomVolcanoPlots markdowns. StatFunctions.R will have the color and axis changes in the code.
Attachments
Issue Links
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3446 [ 22548 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description | During a meeting Muday lab requested to change the volcano plot colors to a more saturated blue and red. Then the middle would be grey instead of black. They also requested to hav all of the x-axis (-10,10) including the custom volcano plots. |
During a meeting Muday lab requested to change the volcano plot colors to a more saturated blue and red. Then the middle would be grey instead of black. They also requested to have all of the x-axis (-10,10) including the custom volcano plots.
Note: These changes need to be implemented with all of the other FindControlVsStress & MakeCustomVolcanoPlots markdowns. StatFunctions.R will have the color and axis changes in the code. |
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!
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
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] | Robert Reid [ robertreid ] |
| Assignee | Robert Reid [ robertreid ] | Ann Loraine [ aloraine ] |
Pulling branch to my local for review.
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.
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.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
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.