Difference between revisions of "Talk:Addon:DNASegmentMapGramplet"

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--[[User:GaryGriffin|GaryGriffin]] ([[User talk:GaryGriffin|talk]]) 22:43, 15 October 2022 (UTC)
 
--[[User:GaryGriffin|GaryGriffin]] ([[User talk:GaryGriffin|talk]]) 22:43, 15 October 2022 (UTC)
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One more update: Michal comment states that there is an undocumented feature. I think this is documented as:
 +
 +
'''Create a Note in the Association or attached to a Citation in the Association with the shared DNA segment data.'''
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I have a draft update that I can provide for testing. It addresses the following issues:
 +
* Fix maternal/paternal calculation when there are shared parents. Currently it chooses maternal.
 +
* Grey out the paternal X chromosome if the active person is male.
 +
* Add an optional field to the chromosome line. It has two possible uses:
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** M/P/U (maternal/paternal/unknown) flag to each chromosome line. This will produce potentially wrong info if you use SyncAssociations since the Note is shared. That is, the forced M/P/U flag persists on the reverse relationship.
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** If the field is any other string, it will be used as a comment field for the tooltip.
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* Add start and stop values to the tooltip.
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 +
Please let me know if you want to test these changes.
 +
 +
--[[User:GaryGriffin|GaryGriffin]] ([[User talk:GaryGriffin|talk]]) 21:51, 16 October 2022 (UTC)

Revision as of 21:51, 16 October 2022

Sam,

Could you revert the filename and the Admin task of deleting the no-longer-needed new filename?

The registration to the Gramplet uses the original Help URL of "Addon:DNASegmentMap", not "Addon:DNASegmentMapGramplet". This just creates extra server load with a redirect.

The "Gramplet" in the filename is redundant. If this page was going to be renamed, it should have be renamed to be more human readable and appear less "code-like" in the header ... with spaces between words.

(cur | prev) 20:36, 20 October 2020‎ Gioto (talk | contribs)‎ m . . (7,331 bytes) (0)‎ . . (Gioto moved page Addon:DNASegmentMap to Addon:DNASegmentMapGramplet: keep gramplet in the name) (undo)

Bamaustin (talk) 18:34, 17 November 2020 (UTC)

---

Michal Maňas had difficulties posting here. Posting on his behalf:

There is also undocumented feature, that the addon is using segment data also from associated citations. I was very surprised, when I found that, because it added segments I was not not expecting. This should be somewhat written to the documentation.

He wonders if a Maternal/Paternal mask could be added.

He also created a Centromere position indicator via a dna segment map"


1,121535434,124535434,0,0
2,92326171,95326171,0,0
3,90504854,93504854,0,0
4,49660117,52660117,0,0
5,46405641,49405641,0,0
6,58830166,61830166,0,0
7,58054331,61054331,0,0
8,43838887,46838887,0,0
9,47367679,50367679,0,0
10,39254935,42254935,0,0
11,51644205,54644205,0,0
12,34856694,37856694,0,0
13,16000000,19000000,0,0
14,16000000,19000000,0,0
15,17000000,20000000,0,0
16,35335801,38335801,0,0
17,22263006,25263006,0,0
18,15460898,18460898,0,0
19,24681782,27681782,0,0
20,26369569,29369569,0,0
21,11288129,14288129,0,0
22,13000000,16000000,0,0
X,58632012,61632012,0,0 

and a list of not tested regions:

13,1,19020094,0,0
14,1,19067948,0,0
15,1,20004965,0,0
21,1,9922017,0,0
22,1,16055121,0,0

---

I am not sure I follow. The map is all of the DNA Associated people. I don't understand what is the undocumented feature. I will certainly add it once I understand what it is. Can you provide a sample with expected vs actual results?

I don't understand the untested regions comment. I don't think any of the sources of the DNA data (GEDmatch, FTdna, ...) have regions which are untested. So where exactly did these untested regions come from? And do they apply to all of the associated DNA files (if you have 5 associated people, did all 5 have these same untested regions)? If so, then the simplest way would be to create a dummy person (name of UNTESTED, for instance) with the untested DNA info. That will paint that data. Or am I misunderstanding?

The Maternal/Paternal is determined by the tree itself. I realize this is slightly different than DNApainter uses, because that tool does not also have an associate tree. Initially I coded this with a maternal/paternal flag required for each line (like DNApainter). The downside was each line of each file now had to be editted to add this flag assuming you are cut/paste from GEDmatch or similar. But the relationship of maternal/paternal was per-person, not per-segment. So lots of unnecessary editing . And consider that Gramps already knows the relationship, so why add it again.

In the case where you do not know which side, I can see why you might want to add a M/P flag to the person (not each line). What would be expected if the tree says the connection was on the paternal side and the DNA data had the flag for maternal? I removed the flag for these reasons.

---

I think we are mixing up Chromosome Painting with Chromosome Browsing.

TLDR: Chromosome Painting uses the active person and a vendor-specific reference ethnicity map, whereas Chromosome Browsing uses shared segments between the active person and associated person(s). This gramplet implements the latter.

Chromosome Painting

The new AncestryDNA Chromosome Painter has ‘untested’ segments. As does the FTDNA Chromosome Painter. These tools use the members DNA and compares the Ethnicity mappings that they have collected and paints the segment map appropriately. The ‘secret sauce’ is this ethnicity reference table, which each vendor builds based on the samples they have processed. There are ‘blank’ or untested areas in it. All you get is the ethnic region on the segment map (not a persons name). This is useful for understanding where a particular segment geographically came from, in hopes to indirectly guess on which line it comes from. The maternal/paternal are both painted based on their individual lookup of the Ethnicity map. There is no ambiguity on maternal vs paternal sides, since each side is painted based on the Ethnicity map independently.

Let me exaggerate a point to simplify. If John Doe has a mother who is 100% German and a father who is 100% Irish, the map would have all of the maternal segments one color for Germany and the paternal segments all a different color for Ireland. And there would be grey segments where untested.

The ‘secret sauce’ is proprietary to the vendor, so this really cannot be implemented in Gramps.

Chromosome Browsing

This is not the same as Chromosome Browsing, which is what DNApainter and this gramplet do. The idea for this tool it to compare the active person with shared segments (created by GEDmatch or FTdna or …) of associated people and paint the segments that match, identifying which person maps with the active person. There are no ‘untested’ in this analysis. If the associated person is maternally related (based on the tree), then the maternal chromosome is painted. Conversely if they are paternally related, the paternal chromosome is painted. If the person is not genetically (known) connected, then both are painted (but with transparency).

Example: If John Doe is related to Mary Smith thru his mother, then the shared segments they have would be painted on the segment map on the maternal side. If they are related thru Marys father, Mary’s map would have the paternal segment painted. The more people associated, the more different colors on the map.

If you hover over the shared segment on the map, it will tell you the shared length (in cM). This provides a hint on the genetic distance.

The Shared cM Project has a lookup for relationship to cM range. The ranges overlap significantly for lower cM values. Given a cM value, there is a large range of relationships possible. For instance. for 75 cM , the table from DNApainter (by Jonny Per) is HERE. This is more info than is practical to display, even if it were public domain.

--GaryGriffin (talk) 16:12, 14 October 2022 (UTC)

I created a bug report for all of the recent suggestions: https://gramps-project.org/bugs/view.php?id=12712

Given Michal wanted to add a M/P flag for each line and George wanted a comment for each line:

Proposal: the input format changes from the required fields: Chromosome Number, Start, Stop, cM, SNPs to add an optional 6th field. If the new field is "M" or "P", it will override the tree-determined side of the chromosome. Otherwise the field is considered a comment for the purposes of the tooltip.

Should the override only occur if there is no genetic path between the people (and the tool would otherwise paint both M and P sides)? Or should it even override the genetic path that the tree calculates.

Does anyone have the definitive list of untested segments so that I can grey them out?

--GaryGriffin (talk) 22:43, 15 October 2022 (UTC)

One more update: Michal comment states that there is an undocumented feature. I think this is documented as:

Create a Note in the Association or attached to a Citation in the Association with the shared DNA segment data.

I have a draft update that I can provide for testing. It addresses the following issues:

  • Fix maternal/paternal calculation when there are shared parents. Currently it chooses maternal.
  • Grey out the paternal X chromosome if the active person is male.
  • Add an optional field to the chromosome line. It has two possible uses:
    • M/P/U (maternal/paternal/unknown) flag to each chromosome line. This will produce potentially wrong info if you use SyncAssociations since the Note is shared. That is, the forced M/P/U flag persists on the reverse relationship.
    • If the field is any other string, it will be used as a comment field for the tooltip.
  • Add start and stop values to the tooltip.

Please let me know if you want to test these changes.

--GaryGriffin (talk) 21:51, 16 October 2022 (UTC)