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I'm wanting to create a merged object in Seurat using 2 10x Visium 'slices'. However, when I create an object, Seurat assigns an identity "SeuratProject" to the objects (by default I'm guessing; see attached plot). This will be problematic when I attempt to merge the objects as there will be unintended duplicates of the objects.

Here's what I'm attempting to use to create the 10x Spatial Object:

brain1 <- Load10X_Spatial(data.dir = "~/xxx", filename = "filtered_feature_bc_matrix.h5", assay = "Spatial", slice = "slice1", filter.matrix = TRUE, to.upper = FALSE)

I'd need the ability to assign unique ident to each of these (and any subsequent) slices/data.

Thank you!!

Plot output showing the "SeuratProject" Identity

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1 Answer 1

Reset to default
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You can re-assign orig.ident after creating the object. For example:

brain1 <-Load10X_Spatial(data.dir = "~/xxx", filename = "filtered_feature_bc_matrix.h5", assay = "Spatial", slice = "slice1", filter.matrix = TRUE, to.upper = FALSE)
brain1$orig.ident <- "Visium"
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  • $\begingroup$ Didn't work for me. I don't know what I did wrong. $\endgroup$
    – ROCIO DIAZ
    Commented Aug 26, 2021 at 22:14
  • $\begingroup$ The active.ident is still "SeuratProject", so also add Idents(brain1) <- "Visium". There should be a "project" option in Load_10X_Spatial to change the "SeuratProject" default $\endgroup$
    – Chris S.
    Commented Dec 27, 2023 at 22:01

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