R crashes after analyze(vision) - fitting ...

[rmicheroli]

Hey Matt,

Unfortunately by running analyze(vision), R crashes during/after fitting ...

....
Evaluating local consistency of signatures in latent space...

  |==============================================================================| 100%, Elapsed 00:41
  |==============================================================================| 100%, Elapsed 04:17
  |==============================================================================| 100%, Elapsed 01:49
  |==============================================================================| 100%, Elapsed 00:01
Clustering signatures...

fitting ...
  |=============================================================================================| 100%

and here is the code i use:

library(VISION)
library(Seurat)
seurat <- readRDS("~/Files/seurat.rds")

signatures <- c("~/Files/c7.all.v7.5.1.symbols.gmt")
DefaultAssay(seurat) <- "RNA"
vision.obj <- Vision(seurat, signatures = signatures)

vision.obj <- analyze(vision.obj)

Thanks a lot for your help!

Best,
Raphael

[mattjones315]

Hi Raphael,

Thanks for posting this issue - from the code example, everything looks fine.

I have indeed experienced this issue myself before, and I believe it has to do with the external package that's used to fit the GMM (mclust). From the previous times I've looked into it, the issue has generally been with the cluster environment: specifically, that the shared libraries currently in use were different from those used to build R or mclust. The problem and answers in this post describes the issue more in depth.

I apologize for not being of more help here. But if you find that this is certainly not an issue with your environment but rather the VISION package I'm happy to take a deeper look into it with you.

Thanks,
Matt

[apal6]

Hi,

Thank you for the wonderful package. I have encountered this error and not sure what is happening. Am I doing it right?

library(VISION) #load the seurat object : sobj library(fgsea) hallmark_pathway <- gmtPathways("/path/h.all.v7.0.symbols.gmt.txt") DefaultAssay(sobj) <- "RNA" vis <- Vision(sobj,signatures = hallmark_pathway)

Error:
Importing counts from obj[["RNA"]]@counts ... Normalizing to counts per 10,000... Importing Meta Data from [email protected] ... Importing latent space from Embeddings(obj, "pca") using first 30 components Loading data from JUNB ... Error in readSignaturesInput(sig) : Cannot find file: JUNB

Can you help?

Thank you so much!

[deto]

@apal6 don't load the signatures with 'gmtPathways' first. Instead, just pass the file path to Vision. e.g.

vis <- Vision(sobj,signatures = "/path/h.all.v7.0.symbols.gmt.txt")

[apal6]

Thank you for quick response.

I tried it and now there's a new error

DefaultAssay(sobj) <- "RNA" vis <- Vision(sobj,signatures =signature) Importing counts from obj[["RNA"]]@counts ... Normalizing to counts per 10,000... Importing Meta Data from [email protected] ... Importing latent space from Embeddings(obj, "pca") using first 30 components Loading data from HALLMARK_HYPOXIA ... Error in readSignaturesInput(sig) : Cannot find file: HALLMARK_HYPOXIA

[deto]

Can you show me how you are creating the 'signature' variable?

…

On Fri, Aug 18, 2023, 10:25 AM apal6 ***@***.***> wrote: Thank you for quick response. I tried it and now there's a new error DefaultAssay(sobj) <- "RNA" vis <- Vision(sobj,signatures =signature) Importing counts from ***@***.*** ... Normalizing to counts per 10,000... Importing Meta Data from ***@***.*** ... Importing latent space from Embeddings(obj, "pca") using first 30 components Loading data from HALLMARK_HYPOXIA ... Error in readSignaturesInput(sig) : Cannot find file: HALLMARK_HYPOXIA — Reply to this email directly, view it on GitHub <#119 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEGXRYYCNOS6QJVIRX7Y53XV6QRXANCNFSM5YX2KZOQ> . You are receiving this because you commented.Message ID: ***@***.***>

[apal6]

signatures <- read_tsv("/path/h.all.v7.0.symbols.gmt.txt") head(signatures) DefaultAssay(sobj) <- "RNA" vis <- Vision(sobj,signatures=signatures)

[deto]

no, there you are using read_tsv. You need to pass the file path directly into the Vision function, the way I showed. Use this command:

vis <- Vision(sobj, signatures = "/path/h.all.v7.0.symbols.gmt.txt")

[apal6]

Got it! Thank you, that worked