cbImportSeurat does not work with Seurat4.0.0 objects?

[cotedivoir]

Hi! Tried to run cbImportSeurat and got this error:

Object was created with Seurat version 4.0.0 Error in ExportToCellbrowser : can only process Seurat2 or Seurat3 objects, version of rds is 4.0.0

[matthewspeir]

Hi, @cotedivoir.

Thanks for the report! Sorry for the delay. We'll look into this soon. Would you be willing to share your Seurat 4 RDS with us so that we have a testing dataset when we sit down to investigate Seurat 4 support? If so, you can share a link to it with us at cells@ucsc.edu.

[maximilianh]

Hi Matt, I've allowed Seurat4 objects now in the develop branch. If you have Seurat4 installed, you can use pbmc_small or the pbmc3k object that is part of the tutorial: https://satijalab.org/seurat/archive/v3.0/interaction_vignette.html. It's possible that it just works... fingers crossed. I hope the Seurat authors have not broken compatibility, again...

On Thu, Apr 8, 2021 at 6:38 PM Matt Speir @.***> wrote:

Hi, @cotedivoir https://github.com/cotedivoir.

Thanks for the report! Sorry for the delay. We'll look into this soon. Would you be willing to share your Seurat 4 RDS with us so that we have a testing dataset when we sit down to investigate Seurat 4 support? If so, you can share a link to it with us at @.***

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[matthewspeir]

Your ExportToCellbrowser function doesn't seem to like that an older version of Seurat was used to create the RDS file?

INFO:root:inFname: seurat4.rds, outDir: tmp_seurat4, datasetName: tmp_seurat4
HERE rds
INFO:root:Wrote R script to tmp_seurat4/runSeurat.R
INFO:root:running tmp_seurat4/runSeurat.R through Rscript
Loading required package: Seurat
Attaching SeuratObject
Reading seurat4.rds as .rds file
Exporting Seurat data to tmp_seurat4
Seurat Version installed: 4.0.1
Object was created with Seurat version 3.1.4
Error in ExportToCellbrowser(sobj, "tmp_seurat4", "tmp_seurat4", markers.file = NULL,  : 
  The installed version of Seurat is different from Seurat object loaded. You have to down- or upgrade your installed Seurat version, see the Seurat documentation
Execution halted

[maximilianh]

Yes you need to save the object with Seurat 4, not 3.

On Fri 9 Apr 2021 at 18:37, Matt Speir @.***> wrote:

Your ExportToCellbrowser function doesn't seem to like that an older version of Seurat was used to create the RDS file?

INFO:root:inFname: seurat4.rds, outDir: tmp_seurat4, datasetName: tmp_seurat4 HERE rds INFO:root:Wrote R script to tmp_seurat4/runSeurat.R INFO:root:running tmp_seurat4/runSeurat.R through Rscript Loading required package: Seurat Attaching SeuratObject Reading seurat4.rds as .rds file Exporting Seurat data to tmp_seurat4 Seurat Version installed: 4.0.1 Object was created with Seurat version 3.1.4 Error in ExportToCellbrowser(sobj, "tmp_seurat4", "tmp_seurat4", markers.file = NULL, : The installed version of Seurat is different from Seurat object loaded. You have to down- or upgrade your installed Seurat version, see the Seurat documentation Execution halted

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[maximilianh]

Hmm, there also is this function: https://www.rdocumentation.org/packages/Seurat/versions/3.1.4/topics/UpdateSeuratObject

I don't understand what it does, does it update from seurat 2 to seurat 3? Would it also work from Seurat 3 to Seurat 4? If it does, you could try it? Hey @cotedivoir, do you understand how to convert seurat objects between the different versions?

[matthewspeir]

I saved it in my env with Seurat4 installed, though I had to load it through their SeuratData package, so maybe that's why.

[matthewspeir]

The UpdateSeuratObject worked is updating it to v4.

Seems like cbImportSeurat is happy? It exported the matrix/meta/coords and it's calculating the markers now.

[maximilianh]

Great! This was a lot easier than expected.

On Fri 9 Apr 2021 at 19:39, Matt Speir @.***> wrote:

The UpdateSeuratObject worked is updating it to v4.

Seems like cbImportSeurat is happy? It exported the matrix/meta/coords and it's calculating the markers now.

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[cotedivoir]

Hi! I commented out : if (substr(object@version, 1, 1)!='4' && substr(object@version, 1, 1)!='3') { stop("can only process Seurat2 or Seurat3 objects, version of rds is ", object@version) } in runSeurat which cbImportSeurat generates, and it worked for my Seurat 4 objects

[maximilianh]

Great, yes, that's more or less what I did in the develop version, to accept version 4.

Even better to hear to this worked for you. Matt, I guess we can close the ticket then?

On Fri, Apr 9, 2021 at 11:36 PM Anastasia @.***> wrote:

Hi! I commented out : if @., 1, 1)!='4' && @., 1, 1)!='3') { stop("can only process Seurat2 or Seurat3 objects, version of rds is ", @.***) } in runSeurat which cbImportSeurat generates, and it worked for my Seurat 4 objects

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[matthewspeir]

Sounds good! Let's close it. :)

[RoganGrant]

To clarify, are seurat4 objects supported in any release versions as of now?

[matthewspeir]

We run cbImportSeurat on seurat4 objects all the time.

[RoganGrant]

Thank you! I ended up answering my own question anyway in 1.2.1

[matthewspeir]

Awesome :)