[IGBF-1344] graph operations don't handle inverse 0 well - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
- beginner

Story Points:
0.25
Epic Link:
Improve IGB for users
Sprint:
Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5

Description

Graph tracks can have regions with value=0.
One of the graph track operations is the inverse function, and several other functions include an inverse.
But the inverse of 0 is infinity.
IGB needs to handle this.

Currently, if you take the inverse of a graph track where the value is 0, the y-max for the resulting track is set to 340282346638528860000000000000000000000, and the values on the Y-axis end in "Y", and all the values that have legit values are squished down to be invisible, so the entire track appears blank.

The inverse function just needs to have a catch to handle this. If input is 0, output is NA.

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graphWithNegative.bedgraph
05/Nov/20 10:27 AM
0.2 kB
Nowlan Freese
graphWithNoZero.bedgraph
30/Oct/20 11:38 AM
0.1 kB
Nowlan Freese
graphWithZero.bedgraph
30/Oct/20 11:38 AM
0.2 kB
Nowlan Freese

Issue Links

relates to

IGBF-2134 Fix inverse graph operation problem

Closed

IGBF-1340 Inverse,Log3,Natural Log operation of Track Graph did not show the same result as mentioned in the test wiki doc.

Closed

IGBF-1342 Diff operation on 2 tracks is giving " no point" in ycord value in selection info in Graph Track Operations

Closed

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Nowlan Freese added a comment - 30/Oct/20 11:42 AM

To replicate in IGB:
1) Open human genome (H_sapiens_Dec_2013)
2) Navigate to: chr1:0-550
3) Load the two attached files (graphWithNoZero.bedgraph and graphWithZero.bedgraph) into IGB and load their data.
4) Click the graphWithZero.bedgraph track label to select it.
5) Under the Graph tab within the Operations section, change the Single-Graph dropdown to Inverse and click Go.

Note that this will max out the value of the zero values to 340282346638528860000000000000000000000.
Repeat the same steps for the graphWithNoZero.bedgraph file to observe how the graph should appear.

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Nowlan Freese added a comment - 30/Oct/20 11:42 AM To replicate in IGB: 1) Open human genome (H_sapiens_Dec_2013) 2) Navigate to: chr1:0-550 3) Load the two attached files (graphWithNoZero.bedgraph and graphWithZero.bedgraph) into IGB and load their data. 4) Click the graphWithZero.bedgraph track label to select it. 5) Under the Graph tab within the Operations section, change the Single-Graph dropdown to Inverse and click Go. Note that this will max out the value of the zero values to 340282346638528860000000000000000000000. Repeat the same steps for the graphWithNoZero.bedgraph file to observe how the graph should appear.

4 older comments

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Nowlan Freese added a comment - 17/Nov/20 11:51 AM

Tested on mac using 1344 dmg installer from Supreeth's branch.

Tested using attached test files. Working correctly.

Sai Supreeth Segu ready for pull request.

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Nowlan Freese added a comment - 17/Nov/20 11:51 AM Tested on mac using 1344 dmg installer from Supreeth's branch. Tested using attached test files. Working correctly. Sai Supreeth Segu ready for pull request.

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Sai Supreeth Segu (Inactive) added a comment - 17/Nov/20 11:54 AM - edited

[~aloraine] - Please review my pull request
Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/849/igbf-1344-fixing-inverse-0-value

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Sai Supreeth Segu (Inactive) added a comment - 17/Nov/20 11:54 AM - edited [~aloraine] - Please review my pull request Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/849/igbf-1344-fixing-inverse-0-value

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Sai Supreeth Segu (Inactive) added a comment - 18/Nov/20 11:49 AM

Dr. [~aloraine] and Dr. Nowlan Freese, I have updated the pull request with a commit. Please review the pull request.
Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/849/igbf-1344-fixing-inverse-0-value

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Sai Supreeth Segu (Inactive) added a comment - 18/Nov/20 11:49 AM Dr. [~aloraine] and Dr. Nowlan Freese , I have updated the pull request with a commit. Please review the pull request. Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/849/igbf-1344-fixing-inverse-0-value

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Ann Loraine added a comment - 28/Jan/21 9:06 AM

Nowlan Freese - please confirm that the requested functionality is implemented in released IGB version 9.1.6.

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Ann Loraine added a comment - 28/Jan/21 9:06 AM Nowlan Freese - please confirm that the requested functionality is implemented in released IGB version 9.1.6.

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Nowlan Freese added a comment - 28/Jan/21 12:26 PM

Tested on release 9.1.6 on Mac using the attached bedgraph files.

Applying inverse to a value of 0 in the graph operations now results in a value of infinity.

Closing issue.

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Nowlan Freese added a comment - 28/Jan/21 12:26 PM Tested on release 9.1.6 on Mac using the attached bedgraph files. Applying inverse to a value of 0 in the graph operations now results in a value of infinity. Closing issue.

graph operations don't handle inverse 0 well

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