[IGBF-3482] Create custom volcano plots for the paper - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
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Story Points:
2
Epic Link:
Prepare flavonoid RNA-Seq time course analyses for publication
Sprint:
Fall 5

Description

Contact Anthony for details. Make sure we know exactly what he wants before starting.

As per our meeting on Friday, we learned that Muday lab wants versions of the volcano plots without any labels on the gene names.

Create a new Markdown that reads the expression analysis results and then creates a support vector graphics format image showing volcano plots of interest. Anthony, or another person in Muday lab, will then open the image in a graphics editing program to add gene names to the points manually. They are doing this because they want specific genes to be shown in the image to illustrate points being made in the paper.

Attachments

Issue Links

relates to

IGBF-3520 Review scale of the Volcano plots regarding the Y axis ( -logPvalue)

Closed

IGBF-3565 Investigate: more up-regulated genes than down-regulated genes

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Activity

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Molly Davis added a comment - 30/Oct/23 3:30 PM - edited

Email Response:

Hi Molly,

I think that as long as we have the plots displaying the temperature dependent DE genes from the final timepoints (75min) for each genotype, without gene IDs on the plot, that would be great! Please let me know if you have any more questions!

Thank you for all of your help!
Anthony

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Molly Davis added a comment - 30/Oct/23 3:30 PM - edited Email Response : Hi Molly, I think that as long as we have the plots displaying the temperature dependent DE genes from the final timepoints (75min) for each genotype, without gene IDs on the plot, that would be great! Please let me know if you have any more questions! Thank you for all of your help! Anthony

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Ann Loraine added a comment - 08/Nov/23 2:41 PM

Thanks a lot [~molly]!
Please proceed with PR when ready.

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Ann Loraine added a comment - 08/Nov/23 2:41 PM Thanks a lot [~molly] ! Please proceed with PR when ready.

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Molly Davis added a comment - 08/Nov/23 2:50 PM

PR: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/33

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Molly Davis added a comment - 08/Nov/23 2:50 PM PR : https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/33

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Molly Davis added a comment - 09/Nov/23 10:43 AM - edited

Testing:

Markdown = MakeCustomVolcanoPlots.Rmd

Muday lab requested plots displaying the temperature dependent DE genes from the final timepoints (75min) for each genotype, without gene IDs on the plot. To do this we made a new markdown that creates custom volcano plots with a custom function. We did this because we did not want to make changes to original functions and markdowns. So this new markdown allows us to take results made from (FindControlVsStressDEGenes-SL4-DESeq2.Rmd -> CvT-DESeq2-SL4.txt) and create custom volcano plots with and without labels at 75min for each genotype.
Please pull down the new markdown (https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/MakeCustomVolcanoPlots.Rmd) and knit the markdown.
If there are no errors with knitting, next check the MakeCustomVolcanoPlots.pdf and CustomVolcanoPlots-SL4-DeSeq2.pdf output files.
Do these files answer to their requests?

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Molly Davis added a comment - 09/Nov/23 10:43 AM - edited Testing : Markdown = MakeCustomVolcanoPlots.Rmd Muday lab requested plots displaying the temperature dependent DE genes from the final timepoints (75min) for each genotype, without gene IDs on the plot. To do this we made a new markdown that creates custom volcano plots with a custom function. We did this because we did not want to make changes to original functions and markdowns. So this new markdown allows us to take results made from (FindControlVsStressDEGenes-SL4-DESeq2.Rmd -> CvT-DESeq2-SL4.txt) and create custom volcano plots with and without labels at 75min for each genotype. Please pull down the new markdown ( https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/MakeCustomVolcanoPlots.Rmd ) and knit the markdown. If there are no errors with knitting, next check the MakeCustomVolcanoPlots.pdf and CustomVolcanoPlots-SL4-DeSeq2.pdf output files. Do these files answer to their requests?

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Robert Reid added a comment - 09/Nov/23 3:52 PM

I pulled code based off of this:

"Please pull down the new markdown (https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/MakeCustomVolcanoPlots.Rmd) and knit the markdown."

I knitted the code with success.
A Pdf was produced.
Many Volcano plots exist with that PDF!

Clearly, the plots are from the 75 min time points.
ANd I clearly see plots with the time points and a subsequent plot without the time plot.

This all looks good to me!

Rob

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Robert Reid added a comment - 09/Nov/23 3:52 PM I pulled code based off of this: "Please pull down the new markdown ( https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/MakeCustomVolcanoPlots.Rmd ) and knit the markdown." I knitted the code with success. A Pdf was produced. Many Volcano plots exist with that PDF! Clearly, the plots are from the 75 min time points. ANd I clearly see plots with the time points and a subsequent plot without the time plot. This all looks good to me! Rob

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Molly Davis added a comment - 09/Nov/23 3:58 PM

Thanks [~RobertReid]

Moving ticket to done!

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Molly Davis added a comment - 09/Nov/23 3:58 PM Thanks [~RobertReid] Moving ticket to done!

People

Assignee:

Molly Davis

Reporter:

Ann Loraine

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Dates

Created:

30/Oct/23 9:44 AM

Updated:

25/Jan/24 3:59 PM

Resolved:

09/Nov/23 3:58 PM