Building a Color Coded Chromosome Mapping Tool

I am starting work on a web based program that will generate color-coded images of the chromosome segments inherited from your ancestors on an image of all 23 of your chromosomes. Cece Moore has done this by hand and that is the model for what this program will do. Click here for the sample image  she posted in her geni.com blog article about autosomal DNA testing

The first release will just take your spreadsheet and make a picture. That spreadsheet will have the same columns as the family inheritance compare at 23andme (or chromosome compare at ftDNA and GEDmatch) plus 3 new columns, side (paternal or maternal), MRCA(s) and optional color choice for each MRCA. Initially 16 ancestors can be plotted. A color palette can be chosen instead of specific colors and that will include a grayscale for the color blind.

So I solicit all your suggestions. I am reposting here some of the thoughts of my fellow DNA-NEWBIE mailing list members, brought to us by ISOGG

 


from Kelly Wheaton of the Wheaton Surname Project “It starts with a blank graphic representation of all 23 pairs of chromosomes each having a top and bottom bar.There is a color coded KEY which you select the color and then type in one of your 16 great great grandparents to represent the color you select.Then there is an entry form where you enter a chromosome, start and stop points and select a color (representing a confirmed GG grandparent) and it paints that on your Chromosome Map. I would suggest all maternal lines in a warm color: Magenta, Red, Pink, Orange, Melon, Yellow, Ochre and Tan. Paternal Lines in Navy, Royal, Sky, Lime, Forest, Grass, Purple, Lavender.”


from Angie Bush of Genes and Trees “I think that it needs to be a visual representation of the chromosomes, not an excel spreadsheet where you map each SNP to a particular ancestor. I’d like to be able to see a paternal and maternal ‘picture’ of each chromosome. It seems to me that so far all of the ch. browsers just show one chromosome. If people see 2 chromosomes, I think the paternal/maternal confusion might be easier to explain.

I think that you should also be able distinguish if you know the shared segment came from only one ancestor, or if it came from an ancestral couple. For example, I’ve tested all of my grandparents except 1 (I know, lucky me :)). I can therefore map certain segments to each one of them. However, I also match distant cousins, and don’t know if we inherited the segment from our common ggg-grandpa OR ggg grandma (although I can pinpoint that segment would have come from their child to me). I think that can be an important distinction.
I would also like to be able map certain ethnicities. For example, I have a grandmother from Romania. I’ve got areas in my results marked as Romanian in Family Inheritance Advanced. I’d like to be able to put hash marks or dots or something over the colored part of my chromosomes from her showing that they’re “Romanian”

Cece Moore our genetic genealogist friend, “I definitely would like it to include the X like 23andMe does. I have also found that longer chromosomes like 23andMe’s representation is easier to keep to scale than FTDNA’s.
23andMe will VERY soon be completely Build 37.
This will be extremely popular. I get requests all of the time when people see mine in my presentations. I used Photoshop and After Effects and do overlays, so most people can’t use my method.”

12 thoughts on “Building a Color Coded Chromosome Mapping Tool

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    • thanks Kelly! So where in California? we are 20 minutes inland from san diego. I have 2 huge avocado trees, 1 60 foot fig tree, 2 tangerines, 2 pomegranites, a lemon, a valencia orange …. plus a few newly planted trees. Also a rose garden, an herb garden, a vegetable garden and much in progress since we have only been here a year!

      • Napa Valley. We have Plums, Apples, Peaches, Walnuts, Berries and melons. Small rose garden, veggies, Potted citrus ( under eaves). This past week we tore out what was left of our lawn so mainly natives, and drought tolerant plants. Some of it is Japanese style- Mediterraneanish. 1 acre which we tend ourselves.

  1. THANK TOU for doing this. I’ve wished I had the programming knowledge to tackle this on my own.

    One suggestion I’d have is to have different views for each generation. For example, click a radio button to get two colors (your parents). Click a different one to get four colors (grandparents) etc.

    I think with javascript you could make a really slick slider bar. That could take you “back” in the time. I’d image father and mother would be red and blue. As you go back in time, paternal lines stay in the warm pallet (reds, yellows, oranges) and maternal stats in the cool palate (blues, purples and greens). With some consistency like that, sliding the generation bar would turn your red/blue parents into a rainbow of different colors, but it would be a little bit intuitive.

    Good luck!

    • excellent thoughts Eric! Thanks. Spelling and all.

      the first version will probably be very simple just a spreadsheet to chromosome map but I like your ideas for the next version!

    • Erik,
      This is an excellent idea. Since the programmer doesn’t know our ancestry, it requires some data input on our part. I have columns for each generation (13 of them) to note the individual ancestors out to the Common Ancestor. I use ahnentafel numbers in lieu of names to keep it compact.
      I ran Kitty’s program on Gen3 and got a map of grandparents; then shifted to Gen4 and got a map of great grandparents; the Gen5…. it easily shows how each generation divided up the genome..

    • Instead of radio buttons, I made a feature where you can specify a different column heading to use for the MRCA. That allows you to have several columns, at different levels of ancestry, in the same file to be mapped. Not as slick but less time consuming for me 🙂

  2. Sounds like a great tool — may I suggest that you make it available in versions that can be read by older excel versions and other spreadsheet programs that can import older excel files?

  3. Thanks Bob, good thought, my plan is to accept a CSV file which most any spreadsheet program can output or read

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