Add rest of Banksy notebook draft#992
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allyhawkins
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allyhawkins
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The code here all looks good to me. I had some very very minor comments but I'm on board with everything you are showing here, so I don't need to see this again.
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| pheatmap::pheatmap(clusters_tab) |
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I have to say I didn't like the version in the outline and thought I was going to tell you to remove this, but I actually think this is much better and worth keeping in.
I do wish there was an easy way to add a column and row title to indicate which clusters are non-spatial vs banksy, but I don't think there is with pheatmap.
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I do wish there was an easy way to add a column and row title to indicate which clusters are non-spatial vs banksy, but I don't think there is with pheatmap.
i really, really, really tried. but didnt manage it :/
| 6 being lowest expression makes sense given that it also corresponds, although less so, to non-spatial cluster 1. | ||
| We have therefore refined our non-spatial clusters with spatial information to give us clusters that consider spatial relationships as well. | ||
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| Anything else you see to point out here? |
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I would keep this section very simple and surface level so what you have here seems good to me.
Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
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Again this notebook is passing CI but we're getting got by #991 |
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Closes #979
Stacked on #984
This PR adds the rest of the Banksy notebook, which is banksy with agf on, more cluster comparisons, and plotting collagen expression across clusters.
Here is the notebook: 02-spatial_clustering.nb.html
Feedback of all kinds welcome!