Error in getSpatialDataset

[Umaarasu]

Hi,

When I run this command
getSpatialDataset(dataset = 'scRNA_mouse_brain', directory = results_folder). I get this error "Error in getSpatialDataset(dataset = "scRNA_mouse_brain", directory = results_folder) :
object 'wrap_msg' not found". Has anyone else had this problem?

[RubD]

Hi @Umaarasu,

What's the version of GiottoData that you're using and can you try re-installing GiottoData again?

packageVersion('GiottoData')

devtools::install_github("drieslab/GiottoData")

[Umaarasu]

Hi @RubD and @mattobny ,

packageVersion('GiottoData')
[1] ‘0.2.1’

Even if I did re-install the GiottoData package and load the library, I get error in the next couple of steps

rank_matrix = makeSignMatrixRank(sc_matrix = get_expression_values(giotto_SC,values = "normalized",output = "matrix"),
sc_cluster_ids = pDataDT(giotto_SC)$Class)
Error in get_expression_values(giotto_SC, values = "normalized", output = "matrix") :
could not find function "get_expression_values"..

Similar issue with Page enrichment..the scran package is not installed along wth giotto and when I do install seperately, it gives non-zero exit status.

[mattobny]

@Umaarasu Hello, wrap_msg() is a function in the Giotto package, i.e. this repository. Loading GiottoData requires loading of Giotto. This should happen automatically, but if you are calling the function without loading the libraries, e.g. GiottoData::getSpatialDataset(), this could be causing the issue.

[mattobny]

@Umaarasu We're going to move this to the issues page, as this seems less like a discussion and more of an issue for troubleshooting. I'll tag you and this discussion in the new issue for reference.