Load_10XSpatial() Error with CytAssist loading #7608
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ejscience
changed the title
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could you please list the output of |
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Hi Team, I have been using Seurat V5 for a few weeks now with no problems loading Visium datasets via "load10X_Spatial" until today when I updated to version Seurat_4.9.9.9058 from Seurat_4.9.9.9041 and SeuratObject_4.9.9.9091 from SeuratObject_4.9.9.9081. Possible bug? looks like a problem with Load10X_Spatial because if I use a workaround that I put together to use ENSEMBL IDs the data loads fine (see code below) Cheers |
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I found the root cause of this error function (data.dir, filename = "filtered_feature_bc_matrix.h5", as you can see, the "image = NULL," is not present as one of the default parameters, therefore, (is.null(x = image)) will always be FLASE, Read10X_Image function is never going to load the image folder. when checking (!inherits(x = image, what = "VisiumV1")), it will never pass, you will always get the error: "Image must be an object of class 'VisiumV1'." the fix is to add "image = NULL," before the three dots to } |
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Hi! I have the same issue but the fixes mentioned above aren't working for me... I have changed the tissue_positions.csv file to tissue_positions_list.csv and it still gives the same error. I checked the tissue_position_list.csv and it looks fine eg Don't know what the issue is, anyone has any idea? These are the directories my files are in: And this is my sessionInfo() |
I did not see how you applied the fix in your code. |
Sorry I meant changing the tissue_positions file name... I don't know how to change the original code so I didn't try doing that. If you can show me how to do it I will try it! I just don't know where I need to change the code, can I do it in my script? |
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@martina-boop did you try something like this (see code below) sorry for the formatting read spatial rnaSeq data with Gene symbol col features.tsvmatrixdir = paste0(filedir,"/filtered_feature_bc_matrix") create seurat object from data dgCMatrixLN15_A1 <- CreateSeuratObject(counts = LN15_A1_data, read Visium image fileimagedir = paste0(filedir,"/spatial") set default assay in image to spatialDefaultAssay(object = image) <- "Spatial" add Visium data to image slotLN15_A1[[LN15_A1]] <- image |
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Hi all, This may be a duplicate of #7560, which I wrote about here. Unless there was an intentional design decision to remove the A Missing ArgumentIt appears the # Install development version `4.9.9.9058` from the remote `seurat5` branch
remotes::install_github(repo = "satijalab/seurat", ref = "seurat5", quiet = TRUE)
packageVersion("Seurat")
#> [1] ‘4.9.9.9058’Note the formal argument names of names(formals(Load10X_Spatial))
#> [1] "data.dir" "filename" "assay" "slice"
#> [5] "filter.matrix" "to.upper" "..."Also note that the names(formals(Read10X_h5))
#> [1] "filename" "use.names" "unique.features"Error:
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Hi all, thank you for your replies! I've ended up using the develop branch and Load10X_Spatial works fine! |
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Thanks for using Seurat! It appears that this issue has gone stale. In an effort to keep our Issues board from getting more unruly than it already is, we’re going to begin closing out issues that haven’t had any activity since the release of v4.4.0. If this issue is still relevant we strongly encourage you to reopen or repost it, especially if you didn’t initially receive a response from us. |
Hello, I have been trying to load a 10X Visium CytAssist counts matrix into a Spatial Seurat object but I keep running into an issue with having the data load. When I submit the data with
It gives me an error of
Then to fix this I try to add an image file by using the following command which outputs a "LargeVisiumV1"
Then when I finally run the
Load10X_Spatialagain I getCan anyone help me figure this out please? I looked it up and only found this link to some people but it did not help this issue.
Here is my sessionInfo for any help
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