Add deconvolution notebook text, part 1#1012
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Jun 5, 2026
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This looks mostly good to me. I just had a few questions of where things could be clarified and then some rewording and small organizational items to address.
| Next, we'll prepare the data for deconvolution by running the function `spacexr::createRctd()`. | ||
| This function sets various values and parameters that will be used for the deconvolution procedure, including: | ||
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| * Identifying genes to use to correct for platform effects |
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How are these identified? Is this from the reference or a combination of the reference and the SPE. I might add some more context here.
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I added some more info to this but tried to not get too into the weeds, aka no big math. Let me know if you think it needs more expansion.
Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
…ore about platform effects
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Towards #1006
This PR fleshes out text in the deconvolution notebook through doublet mode, stopping right when we run full mode.
I expect one more PR to wrap this up.
Let me know if we should add/remove/rearrange any details here.
I also did a bit of rearranging while I was here for flow - originally in the import section, we imported the SPE first and plotted marker gene expression for a set of cell types that are in the reference. I thought it would flow better to read in the reference first which help to contextualize why we're plotting those cell type marker genes on the SPE. So, I just swapped the import order, but no changes to code.