Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Minor
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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:1
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Epic Link:
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Sprint:Spring 3 2023 Feb 1
Description
We want to get Venn Diagram like results for the time series data created via EBSeq-HMM.
We wish to use UpsetR for it's fancy visualization.
Example on how to run UpsetR in R:
{{library(UpSetR)
myGeneSets <- list(
set1 = c("gene1","gene2","gene3"),
set2 = c("gene1","gene4","gene5", "gene7"),
set3 = c("gene1","gene7")
)
upset(fromList(myGeneSets))}}
Run this on the Johnson time series data.
A good location for the ebseq data to go , along with these results would be at the following
Google drive location.
Location for the data on Google Drive:
https://drive.google.com/drive/folders/1_I6PLSoBg4H3Y1MzY2qhxjk-FBmM4cmQ?usp=share_link
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Ann Loraine [ aloraine ] |
| Epic Link | IGBF-2993 [ 21429 ] |
| Description |
We want to get Venn Diagram like results for the time series data created via EBSeq-HMM. We wish to use UpsetR for it's fancy visualization. Example on how to run UpsetR in R: {{library(UpSetR) myGeneSets <- list( set1 = c("gene1","gene2","gene3"), set2 = c("gene1","gene4","gene5", "gene7"), set3 = c("gene1","gene7") ) upset(fromList(myGeneSets))}} Run this on the Johnson time series data. A good location for the ebseq data to go , along with these results would be at the following Google drive location. Location for the data on Google Drive: https://drive.google.com/drive/folders/1_I6PLSoBg4H3Y1MzY2qhxjk-FBmM4cmQ?usp=share_link |
We want to get Venn Diagram like results for the time series data created via EBSeq-HMM.
We wish to use UpsetR for it's fancy visualization. Example on how to run UpsetR in R: {{library(UpSetR) myGeneSets <- list( set1 = c("gene1","gene2","gene3"), set2 = c("gene1","gene4","gene5", "gene7"), set3 = c("gene1","gene7") ) upset(fromList(myGeneSets))}} Run this on the Johnson time series data. A good location for the ebseq data to go , along with these results would be at the following Google drive location. Location for the data on Google Drive: https://drive.google.com/drive/folders/1_I6PLSoBg4H3Y1MzY2qhxjk-FBmM4cmQ?usp=share_link |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Molly Davis [ molly ] |
| Attachment | all_upsetR.png [ 17691 ] |
| Attachment | all_upsetR.png [ 17691 ] |
| Attachment | all_upsetR.png [ 17692 ] |
| Attachment | all_upsetR.png [ 17692 ] |
| Attachment | all_upsetR.png [ 17693 ] |
| Attachment | V2_UpsetR.png [ 17694 ] |
| Comment | [ I tried fixing the numbers at the top bars from overlapping but I think you can only angle them and that didn't work. I can remove them but I think the smaller numbers are important to see. ] |
| Attachment | upsetR_distinct.png [ 17695 ] |
| Attachment | Up-Up-Up_upsetR.png [ 17696 ] |
| Attachment | up_down_up_upsetR.pdf [ 17698 ] | |
| Attachment | down_up_up_upsetR.pdf [ 17699 ] | |
| Attachment | up_up_down_upsetR.pdf [ 17700 ] | |
| Attachment | down_up_down_upsetR.pdf [ 17701 ] | |
| Attachment | up_up_up_upsetR.pdf [ 17702 ] | |
| Attachment | down_down_down_upsetR.pdf [ 17703 ] | |
| Attachment | all_upsetR.pdf [ 17704 ] | |
| Attachment | up_down_down_upsetR.pdf [ 17705 ] | |
| Attachment | down_down_up_upsetR.pdf [ 17706 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| 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 ] |