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Addon:DNASegmentMapGramplet

2,035 bytes added, 20:46, 21 November 2020
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{{languages|Addon:DNAgrampletDNASegmentMapGramplet}}
{{Third-party plugin}}
[[File:Addon-DNA-SegmentMap-with-Tooltip.jpgpng|thumb|450px|right|Example [[Gramps_{{man version}}_Wiki_Manual_-_Gramplets#The_split-screen_Sidebar_.26_Bottombar|Undocked]] {{man label|DNA Segment Map Gramplet}} with the HighContrast [[Addon:Themes|theme]]]]The {{man label|DNA Segment Map Gramplet}} shows a DNA segment map as a graph.
=Usage=
You can install the {{man label|DNA Segment Map Gramplet}} on the bottombar of one of the people or relationship category list views.
==Create a DNA Association==
To specify shared DNA segments between 2 people,
* Create an Association for one person (Person A) with another Person (Person B) of the type DNA.
* Create a Note in the Association of Type: "or attached to a Citation in the Association Note" with the shared DNA segment data.** The format of the Note is a comma separated list or a tab separated list in the order: <code>[https://wikipedia.org/wiki/Chromosome#Human_chromosomes Chromosome Number], Start Segment, End Segment, shared length in [[Genealogy_Glossary#centimorgan|centiMorgans]] (cMs), [https://wikipedia.org/wiki/Single-nucleotide_polymorphism SNP ] (optional)</code>. ** ege.g.: <code>3,56950055,64247327,10.9,1404</code> Which means; Chromosome Number: 3, Start Segment: 56950055, End Segment: 64247327, shared length in cMs: 10.9, matching SNPs: 1404</code>
** Valid entries for each are:
;Start Segment: The starting number for the segment location.
;End Segment: The endinging ending number for the segment location.
;Shared length in cMs: The Genetic Distance (otherwise known as the number of centiMorgans ) in the segment.
;SNP: optional field of the matching SNPs (Single Nucleotide Polymorphism) in the segment.
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===Getting the chromosome data ===
Sites like [https://www.gedmatch.com/login1.php GEDmatch] make this shared chromosome data available. Direct copy from the GEDmatch results page (with header and tab separators) will work. There can be additional Associations between Person A and Person C (et cetera ) as known. [https://dnapainter.com/help/matchdata DNApainter] provides a description of how to get the chromosome data from many of the common sites.
===Legend===
[[File:Addon-DNA-SegmentMap-legend.png|thumb|338px|right|[ {{man label|Legend with rollover tooltip]]* For each Chromosome : the top portion is the Paternal side and the bottom portion is the Maternal side.
* The chromosome segment side (Paternal or Maternal) is determined from the Most Recent Common Ancestor. If there is no common ancestor, both sides are used.
* Hovering the cursor over a painted chromosome segment will show a tooltip with the name of the associated person, ID, length in cMs (centiMorgans) of the shared segment, and matching SNPs of the segment if provided.
* The color code for each associated person in the DNA segment map is consistent but not user-specified. The first Association will always be the same color.
 
===Navigation===
* The Legend on the right side lists each associated person who has a mapped segment. Hovering over the legend items will show a tooltip for possible action. Primary button click will change the active person. Secondary button click will open the Person Editor for the associated person.
===DNA Example data===
To reproduce the illustration with the [[Example.gramps]] dataset, create two records in the Associations of type DNA tab in the Person Editor for Luther Robinson(I0656).
The first record is DNA Association for type, adding an association with Robert F. Garner (I1123).<br />The Note under this association contains the following text:
Chromosome,Start Location,End Location,Centimorgans,Matching SNPs,Name,Match Name 3,56950055,64247327,10.9,375,Luther Robinson, Robert F. Garner
11,25878681,35508918,9.9,396
12,129481599,133491098,12.4,304
6,6179882,15400114,18.5,1994
 The second record is for the also DNA Association of type, adding an association with Maude Garner (I0651).<br />The Note under this association contains the following text:
1,30578594,38686908,11.2,334
21,14670124,18743733,10.8,201
{{man tip|DNA match row data must be in a specific CSV order|The data may include a header but the Gramplet does not require one. Headers are to make the rows more readable by humans. The rows do not need to be sequentially ordered by the chromosome identifier (1 to 22 and X).}}
 
[[File:Addon-DNA-GEDmatch.png|thumb|600px|right]]
Sample GEDmatch output (see screenshot) that can be cut and paste into the Note. The fields are the same - Chromosome, Start, End, cM, and SNPs. This can be cut/paste from the GEDmatch output directly into the Note for the Association. The header line will be ignored.
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=== Example ===
[[File:Addon-DNA-Note-Example.png|thumb|600px|right]]
Create an Association of type DNA as described in the [[Gramps_{{man version}}_Wiki_Manual_-_Entering_and_editing_data:_detailed_-_part_1#Associations|Association]] page to Person A. Add a Note with the DNA shared segment data. Set the Note private if you do not want the data printed in reports.
 
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[[File:Addon-DNA-Association-Example.png|thumb|600px|right]]
Save the Association.
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[[File:Addon-DNA-Associations-Example.png|thumb|600px|right]]
Add more associations as known. Each would be associated to a different person and have a different Note. Since the Associations are drawn in order, it is generally better to have them in order of closest relative to furthest relative to avoid obscuring a distant relative (smaller segment) by a close relative (larger segment). Use the up-arrow and down-arrow to change the order of the Association.
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[[File:Addon-DNA-SegmentMap.png|thumb|600px|right]]
Add the DNA gramplet to the Person view. Select the DNA tab. The segment map will be color coded by associated person. For each Chromosome the top portion is the P (Paternal) side and the M (Maternal) side is the bottom portion. If the chromosome segment side (Paternal or Maternal) is unknown, the segment will cover both the top and bottom portions of the chromosome and be 50% transparent.
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 [[File:Addon-DNA-SegmentMap-with-Tooltip.jpgpng|thumb|600px|right]]
Hovering the cursor over a known segment will pop up the name of the associated person and the length (in cMs) of the shared segment.
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= Issues =
* If the Chromosome Number is not in the range (1, 2, ..., 22, X) it is ignored.
* To create a segment map for Person A, you need to add associations to Person A. There is no reciprocal relationship for Person B - that is, there is no segment map for Person B, only for Person A. You can execute the [[Addon:SyncAssociation]] addon to create any missing reciprocal relationships.
* Color code for each associated person in the map is consistent but not user-specified. The first Association will always be the same color.
* Help link goes to https://gramps-project.org/wiki/index.php?title=Gramps_5.1_Wiki_Manual_-_Gramplets#DNA
* If there are overlapping segments within a maternal/paternal view of a chromosome, only the front (last drawn) will be pickable. If it is completely obscured, you will not be able to see the details of the hidden segment. Changing the order of Associations (using the up-arrow and down-arrow) to have the closer relatives before further relatives will fix this.
= See also =
* DNA Segment Map gramplet #469 (GitHub pre-release [https://github.com/gramps-project/addons-source/pull/469 Pull 469])
* [[Addon:SyncAssociation]] - For every Association, if there is not a reciprocal Association then it will be created. That is, where Person John Smith has a DNA Association (with an Association Note) to Person Jane Jones, then if Jane Jones does not have a corresponding DNA Association to John Smith, it will be created which shares the Note.
* [[Add Types to the SyncAssociation Gramplet]]
* [https://gramps.discourse.group/t/updated-dna-gramplet-ready-for-review/807 Discourse forum discussion on the DNAgrample]
* [[Gramps_{{man version}}_Wiki_Manual_-_Entering_and_editing_data:_detailed_-_part_1#Associations|Introduction to Associations in Gramps]]
* [[Roles, Relationships & Associations]]
* [[Genetics]]
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