Comments (5)
Hi @aditisk,
By default, assay
parameter is set to SCT
, so if you are working with an RNA
assay, you will have to use assay = "RNA"
every time you use the function.
Then, using it alongside the feature you want to plot should work. If not, please send me the code you are using.
Best.
Enrique
from scpubr.
Hi @enblacar, I was already specifying assay="RNA
but it doesn't seem to work for me. Please see the code below:
SCpubr::do_RidgePlot(sample =sample,feature = "LAG3",assay = "RNA") Error: 'SCT' is not an assay
from scpubr.
Hi @aditisk,
I found the source of the error. It is an internal bug in the code in which SCT
assay was hardcoded by mistake. Is it fixed in the last commit and will also be fixed in the next CRAN update. In the meantime, I offer you the following solution:
devtools::install_github("enblacar/SCpubr", ref = "088f20b2027bacefcf6e38d50e3b373e734ec094")
As always, please have in mind that development versions might also contain other bugs, so once you are done with this specific plotting, revert back to the CRAN version of SCpubr
.
I am closing this Issue by now. Let me know if this fixed your issue!
Thanks for this valuable feedback!
Enrique
from scpubr.
Hi @enblacar, I used the version you mentioned above and it works. Thanks :)
from scpubr.
All the changes have been implemented in SCpubr v1.0.3, currently available on CRAN.
Best,
Enrique
from scpubr.
Related Issues (20)
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- Where is the function do_AzimuthAnalysisPlot HOT 1
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- Do_FeaturePlot | Set custom scales/limits OR copy Seurat::FeaturePlot keep.scale parameter HOT 2
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