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March 11, 2026 21:32
allyhawkins
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Overall I think this looks pretty good. I just had some minor wording suggestions throughout, but I think most of the content is there.
spatial/01-spatial_intro.Rmd
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| By default, this function only plot spots that overlay tissue (i.e. where `in_tissue` is 1) and ignore spots that do not overlay tissue. | ||
| We can override this if we want, but again, what we really want to do is actually remove those spots entirely. |
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| By default, this function only plot spots that overlay tissue (i.e. where `in_tissue` is 1) and ignore spots that do not overlay tissue. | |
| We can override this if we want, but again, what we really want to do is actually remove those spots entirely. | |
| By default, this function only plots spots that overlay tissue and ignores spots that do not overlay tissue. | |
| `Space Ranger` determines which spots overlay tissue using the fiducial alignment frame, which we saw in the `"aligned_fiducials.jpg"` image. | |
| Any spots that do not overlay tissue are indicated with a `0` in the `in_tissue` column of the `colData`. | |
| We can override this if we want, but we really want to remove those spots entirely. |
An alternate suggestion for when to talk bout the tissue overlay. I think this makes more sense since you're about to go into it in the next section.
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I like this idea generally, but I still think I'll point out the in_tissue column just with fewer details before.
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The overall content here looks good. My suggestions are mostly minor and formatting related, but a few wording suggestions too.
Co-authored-by: Ally Hawkins <[email protected]> Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: Ally Hawkins <[email protected]>
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Closes #944
Stacked on #949 (gha will run once unstacked, and I can catch any lingering typos then)
This PR fleshes out text for the intro, import, and intro viz sections. While I was here, I referred somewhat to our scRNA-seq 04 notebook and caught a couple tiny things to fix there along the way.
Please let me know about: