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CRI-iAtlas / iatlas-app

R Shiny app for CRI iAtlas, an interactive web portal for exploring immuno-oncology data. (iAtlas portal 2022 and beyond)
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Dataset Overview > Category Key > Incomplete Order values for Race category #167

Closed tschaffter closed 3 months ago

tschaffter commented 2 years ago

The column "Order" in the table is missing values when selecting Race. This seems to be an odd case as most of the other category I selected have a full column "Order" with value sorted in ascending order. I haven't tried all category values.

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andrewelamb commented 2 years ago

@heimannch Could you comment on what the order is here? I know some classes of features have an order for plotting purposes, such as Cibersort results. Did we start adding order to groups such as gender and race at some point?

heimannch commented 2 years ago

I did, for the ICI tags. The main reason to do that was that we have several categories that are ordered (eg. response annotation with levels that ranges from Complete Response -> Progressive Disease) and the plots should follow this order. I think in the case in the screenshot, the order didn't propagate to tags that were already present in the CG datasets.

andrewelamb commented 2 years ago

Should we assign orders to tags where some on the group have an order and some don't? I think only the ICI modules make use of tag order.

heimannch commented 2 years ago

Yeah, that's a good solution. I imagine that this issue will be present with other categories that are present in TCGA and PCAWG, and in the ICI datasets have an extra level of "other"/"not available"/ "unknown" that would look best in the last rows of this table.

andrewelamb commented 2 years ago

Ok I'm not going to assign this to the 2.0 milestone since it's not pressing. We can return to it after we release 2.0.