[IGBF-3643] Testing out the NEW venn diagram style that are circular - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Trivial
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Support NSF pollen grant
Sprint:
Spring 6, Spring 7

Description

In Kelsey's March presentation, she showed a new way to display Venn Diagrams, that a re similar to UpSetR plots but are circular.

I inquired how these were made and she shared the tool as seen in the email below.
It would be worth trying this out and possibly adding it to our toolset repertoire.

GOAL: To test this tool out on some tomato data.

Hi Rob,

Absolutely! I am happy to share. I used the SuperExactTest package in R to calculate the p-values of the overlapping DEGs among cultivars. This tutorial was very helpful to use and essentially "plug in" my data. The "total" number of genes I used was 34,075, based on the number of genes in SL4.0.

Feel free to let me know if you would like to see my code or if you have any thoughts or questions!

Best,
Kelsey

Attachments

Options
- Sort By Name
- Sort By Date
- Ascending
- Descending
- Thumbnails
- List
- Download All

Attachments

c.elegans_data_analysis_slides.png
156 kB
26/Mar/24 9:02 AM

Activity

Ascending order - Click to sort in descending order

Robert Reid created issue - 11/Mar/24 9:05 AM

Robert Reid made changes - 11/Mar/24 9:05 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Robert Reid made changes - 26/Mar/24 9:02 AM

Attachment

c.elegans_data_analysis_slides.png [ 18297 ]

Hide

Permalink

Robert Reid added a comment - 26/Mar/24 9:27 AM

I gave this task to the Grad student Chinaza (He will be joining Liz's lab in May) to try out and he got it to work.

I think it looks cool but one can argue that the circular plot is a bit hard to read when compared to an UpsetR plot.
And on the left side where you have a plot similar to UpsetR, it is misleading. The height of a bar is a summed value, different than how upsetR presents the data.
(Poor explanation I know!)

Show

Robert Reid added a comment - 26/Mar/24 9:27 AM I gave this task to the Grad student Chinaza (He will be joining Liz's lab in May) to try out and he got it to work. I think it looks cool but one can argue that the circular plot is a bit hard to read when compared to an UpsetR plot. And on the left side where you have a plot similar to UpsetR, it is misleading. The height of a bar is a summed value, different than how upsetR presents the data. (Poor explanation I know!)

Hide

Permalink

Robert Reid added a comment - 26/Mar/24 9:46 AM

Asking for a code example from Chinaza. Will share it here once I get it.

Show

Robert Reid added a comment - 26/Mar/24 9:46 AM Asking for a code example from Chinaza. Will share it here once I get it.

Ann Loraine made changes - 01/Apr/24 10:16 AM

Sprint

Spring 6 [ 190 ]

Spring 6, Spring 7 [ 190, 191 ]

Ann Loraine made changes - 01/Apr/24 10:16 AM

Rank

Ranked higher

Ann Loraine made changes - 01/Apr/24 11:13 AM

Assignee

Ann Loraine [ aloraine ]

Robert Reid [ robertreid ]

Hide

Permalink

Robert Reid added a comment - 03/Apr/24 1:28 PM - edited

Given that this tool is simply a different way to view a Venn Diagram or UpsetR Plot, it is best to just use UpsetR plots instead.

Case Closed!!!

Show

Robert Reid added a comment - 03/Apr/24 1:28 PM - edited Given that this tool is simply a different way to view a Venn Diagram or UpsetR Plot, it is best to just use UpsetR plots instead. Case Closed!!!