Comments (2)
MarcElosua
commented on August 17, 2024
Hi @MirDom
Thank you very much for your interest in SPOTlight!
Your issue here is that you are trying to use the ggcells() function which is part of the scater package. This functino doesn't accept Seurat objects as an input, hence the error:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘spatialCoords’ for signature ‘"Seurat"’.
For Seurat I suggest using the standards FeaturePlot() function to plot it,
Hope this helps,
Marc
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Han117
commented on August 17, 2024
Hi Marc,
I found datas (allen_cortex_dwn.rds、markers_anterior.RDS、spotlight_ls_anterior.RDS、tissue_lowres_image.png) in your SPOTlight-spotlight-0.1.7 project on github, but the posterior data and its spatial slices are missing.
I am looking forward to your posterior data and its spatial slices.
When we analyze the anterior and posterior of ST data, both using scRNA-seq allen_cortex_dwn.rds ?
Should we analyze adult mouse anterior ST data and posterior ST data using the same scRNA-seq data（ allen_cortex_dwn.rds ）?
best wishes!
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主题: Re: [MarcElosua/SPOTlight] residuals of the sum of squares doesn't work for Seurat object (Issue #101)
Hi @MirDom
Thank you very much for your interest in SPOTlight!
Your issue here is that you are trying to use the ggcells() function which is part of the scater package. This functino doesn't accept Seurat objects as an input, hence the error:
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Related Issues (20)
- In README.md the processed object can not find HOT 2
- Regarding the PBMC (GSE133549) dataset used in the method HOT 1
- scatter plot circles instead of sctter pie circles HOT 1
- Prepare for upcoming Seurat v5 release
- How to plot specific cell type proportions in the newest version of spotlight? HOT 1
- SPOTlight_1.0.0 on Bioconductor .zip cannot be downloaded
- dplyr::mutate() Error HOT 2
- downsample_se_obj HOT 1
- Questions about some details in paper HOT 2
- Fixed Matrix version incompatible with SeuratObject HOT 1
- Passing dataframe with NAs into plotCorrelationMatrix HOT 1
- Error from `.extract_counts()` when calling `SeuratObject::GetAssayData()` v5.0.1 HOT 1
- assay %in% SeuratObject：：Assays（x） is not TRUE HOT 2
- How to annotate a spot as a type of cell HOT 1
- Error in .extract_coord(x = x, slice = slice, img = img) : !is.null(colnames(x)) is not TRUE HOT 1
- Scatterpie
- HELP! imgData is not equal to the spatialcoords
- trainNMF error HOT 7
- Subset Cells in ScatterPie HOT 1
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