Comments (2)
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
from spotlight.
from spotlight.
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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