Add cellassign organs to report #609
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I think we should update the parsing and and present both. |
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Please also note I am prepared to die on the hill of using the Oxford comma. |
Actually, would we even need to do any sort of parsing here at all? Or just say, "here's the name of the reference we used and it contains these tissue types." |
Co-authored-by: Joshua Shapiro <[email protected]>
If there is nothing additional, no, we don't need to parse it. |
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| methods_text <- glue::glue( | ||
| "{methods_text} | ||
| * Annotations from [`CellAssign`](https://github.com/Irrationone/cellassign), a marker-gene-based approach ([Zhang _et al._ 2019](https://doi.org/10.1038/s41592-019-0529-1)). | ||
| Marker genes associated with `{tissue_type}` tissue were obtained from [PanglaoDB](https://panglaodb.se/).\n | ||
| " | ||
| Marker genes associated with the following tissue types were obtained from [PanglaoDB](https://panglaodb.se/): {organs_string}.\n" |
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PangaloDB call the column organ, so I don't think we want to call it "tissue types". But "organ" seems wrong too. Maybe "Marker genes for cell types categorized to the following organs were obtained from PanglaoDB"
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I have deleted and re-written like 4 sentence versions over here, so I'll take any wording suggestions I can get!
…elman/589-organs-to-report
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Updated phrasing in 4828bce ... eh? feedback suuuper welcome. |
Co-authored-by: Ally Hawkins <[email protected]>
Co-authored-by: Ally Hawkins <[email protected]>
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One other thing, I'm going to have to do another release for cell typing to account for the memory/ cpu increases before we can complete processing objects. Maybe you can file a PR with the changes from this and #608 to |
…eport Add cellassign organs to report
Stacked on #608Closes #589
Here, I've updated the cell type report to include organs. It turns out our current parsing of the reference name would not work well for all of our new references (e.g.
adrenal-pancreas-reproductiveorbone-and-soft-tissue), so I decided to just scrap that code altogether, figuring the tissues/organs are more important than our internal reference name. Yes/no?Here's a screen shot example of how this part of the cell type report now looks!