sairum / tcsbu Goto Github PK

I have a dataset of 1480 individuals that i want to visualize 2 ways (dividing into 19 groups corresponding to locality and 2 groups corresponding to species). I can load the TCS graph file and visualize the network but when I try to load the haplotype file to designate the groupings it fails to load. I get no change in the groupings (everything default) but it seems to load fine.

Any help would be appreciated.

Hi @sairum,

Really neat tool, it is very useful but I am having issues with the colors in the legend which do not correspond to the colors I have assigned. I've attached a screenshot and the input files.

I'd be really grateful if you could help.
Thanks,
Joseph

CalssificationGroups.txt
HaplotypeGroups.txt
TCS_network.txt

Hi! Awesome program. I am curious though - the circles representing the haplotypes seem to scale by the diameter of the circle, rather than the area of the circle like how most people are used to seeing haplotype networks. This means that a haplotype with double the frequency is a circle with twice the diameter, but this makes the circle more than twice as large in area, Is there any way of making the circle area, rather than the circle diameter proportional to the frequency of the haplotype?
Many thanks!

Greetings,

Exploring your program and noticed a couple things, probably related to my ignorance. I have high hopes your systems capability grows.

1. You can remove edges on either side of a node, which then floats away. I was expecting it to delete itself.
2. One cannot reconnect nodes, ergo, move connections or trim excessive nodes.
3. The taxa I am working with exhibit IBD / IBT and the number of nodes needed to connect clades is on the order of 50-100. This looks like a horrible mess of spaghetti on screen. The interface lags noticeably.
4. Support collapsing edges/nodes ala hash marks, or numeric?
5. The detangling process doesn't go to completion; it reaches a stable state where charges balance out in loops. What I did figure out is decreasing charge to ~ -350, decreasing edge length, decreasing elasticity to ~80, and increasing gravity to 1.4. Then it detangled pretty well. It worked so well it might become a singularity if I increased gravity any further.
6. Can you add gis support? :)

Warm Regards,
Nick

Hello,
I am having trouble labeling my chart. I add the labels then I click on the next one and it reverts back to the old name. I also cannot find a way to put the labels on the chart. But the biggest problem is saving. I have saved the SVG code but I am unable to save the image or move it for my publication. I have tried to convert the SVG code but that attempt failed.
Thank you,
Krista

Hi there,
In my data I have individuals that have more than one haplotype (the way that I'm defining haplotype is that each allele is a haplotype). For example, individual A might have 3 alleles (haplotypes) and thus be listed under three separate sequences in the graph file.

However I'm having trouble representing this in tcsBU.

Attached is a mock up file. I took the tcs output graph example and altered it so that "Seq2" (equivalent to one individual for the purposes of my data) shows up as belonging to both the first and second haplotype sequence in the graph file.

When I do this, Seq2 is listed twice in the data panel on tcsBU but I cannot label the second instance of it-- it remains "Default" and grey.

tcs_example_altered.graph.txt

Thanks so much for any insight you can provide. Apologies in advance if I've missed something very obvious.