Closed JiawenChenn closed 4 months ago
Hi @JiawenChenn,
In general, it's best to use reprex::reprex()
as discussed in this video https://www.youtube.com/watch?v=8bBo3B7N8YQ. Check also https://reprex.tidyverse.org/.
Also, with SpatialExperiment
objects, users are not supposed to use the @
accessor function. I'm aware that Seurat
encourages this practice, but in the Bioconductor world the advise is to not use @
, as the internals of an object can change whereas the accessor functions such as colData()
will follow https://contributions.bioconductor.org/deprecation.html and other guidelines that give users time to adjust code if needed.
Now, it seems that you are downloading the data from https://doi.org/10.1101/2023.02.15.528722 which has no manual annotations except for the 4 Visium ImmunoFluorescence (IF; also known as Visium SPG) samples. I believe that you wanted to download the data from https://doi.org/10.1038/s41593-020-00787-0. That is, spatialLIBD::fetch_data("spe")
https://research.libd.org/spatialLIBD/reference/fetch_data.html.
Best, Leo
Hi @lcolladotor,
Thanks a lot!! Thats really helpful.
Best, Jiawen
Hi,
Thanks for organizing the data. I have tried to use the spatialDLPFC_Visium data downloaded using spatialLIBD package. I saw a discussion about the manual annotation in the data. Just want to confirm whether I am using the right name for the annotation.
Are there manual annotation for other slides? Thanks a lot!