Comments (22)
@cclarkson here's some food for discussion tomorrow:
...this is a clustering of haplotypes carrying L995S. Only distinct haplotypes are used to construct the tree. Haplotype frequencies are shown in the adjacent bar plot. Shaded regions show the 5 largest clusters by a method I'll explain tomorrow - I'm thinking we show one network for each of these 5 clusters.
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Hey @cclarkson, maybe Python is an option after all, I made this with graphviz:
cc @hardingnj.
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That's great, will be cool if we could keep most of it in python. Looking forward to seeing the code.
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Making some progress, here's a network with some real data, the Kenya/Uganda L995S cluster:
Will turn this into a usable function and share asap.
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Still not sure how to figure out which edge has which mutation, that may be tricky...
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Hi @alimanfoo ,
Just to document the TCS comparison, almost all clusters produced identical networks to your function, except for 995F8, which TCS did not circularise and 995F16, which added a number of loops compared to the one you generated - see below (I tried to lay it out the same to compare but TCS kept crashing, this is best I managed, the bottom right hand corner is a bit messy!).
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Thanks Chris. Can you compare with the networks I made using median-joining? They should be in the (recently updated) hapclust_demo notebook, look out for the calls to graph_haplotype_network(..., network_method='mjn')
. What you have above in TCS looks very similar to what I made with MJN...
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Yep, I'm pretty sure that is the same as the TCS one, interesting.
ION - having a problem getting graphviz to work due to neato - how did you fix that problem?
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No worries, think I've cracked it.
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Hi @alimanfoo ,
Now I've got this all up and running again, I was just trying to plot multiple networks on one figure but I'm struggling. I can't see how to get it to use an 'ax', is this because it is just a wrapper for external code and can't talk to matplotlib?
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Hi @alimanfoo ,
I'm trying to find a nice way to bring the dendrogram together with the clusters but I'm struggling to work out how to give the fig_haplotypes_clustered function (from haplclust_utils) an ax to plot on in my composite figure because the dendrogram function is already a composite figure. Any pointers would be gratefully received!
Cheers, C.
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Been flailing at this for a while and I think I am finally getting somewhere! I'm now trying to work out how to colour the network's backgrounds like the dendrogram (and align/scale things in a less awful way).
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As far as I can see, the importing of the graphviz image as an image array means that you can't overlay or 'draw' on top of those arrays. I'm going to try an kick out the graphviz stuff in a vector format so that I can build something a bit like this:
I think this figure could then be quite small, losing the fine network details, but we could have individual figures for the clusters of interest. What do you think?
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Hi @alimanfoo,
This was what I was trying to do with just code, but I resorted to a bit of Inkscape in the end. Looks okay, but we would need to make it clear that the network nodes are not to scale across networks, they are just relative to that cluster. Just going to make the stand alone for cluster 16.
-Should I push on with this format for 995S?
-What do you think about leaving the colony haplotypes in this analysis?
-At some stage I saw the network function able to add the size of node (number of haps) to the figure, I'm trying to find this to make a size key, is it still there?
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Hi @alimanfoo
Not sure how I feel about the overlapping nodes, but they can all be re-arranged nicely in Inkscape if we decide to use this type of figure...
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Figure 2 (draft) - haplogroup distance and frequency
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Related Issues (20)
- Check MD OK for Ag1000G RFC
- Ag1000G RFC
- Discussion subsection - resistance phenotype prediction HOT 1
- Address comments from Ag1000G HOT 1
- bioRxiv submission HOT 4
- Discussion of DDT and pyrethroid classes HOT 2
- Discussion - open questions HOT 4
- Discussion final paragraph?
- .
- Final proofing
- Review methods
- In text citation order HOT 2
- Acknowledgments
- Haplotype group assignment issue re F3/F4 HOT 2
- Biorxiv resubmission HOT 2
- PLOS Genetics submission HOT 2
- PLOSgen formatting - citation style = vancouver
- PLOSgen formatting - author attributions - equal contributors HOT 1
- PLOSgen formatting - supp figure title
- re-frame VGSC paper - less Anopholocentric - for resubmission
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