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Description
When I am running the full version of cluster_map, I am getting a circos plot but not able to get the recolored t-sne or separatability:
I am getting the following error:
Error in object[[reduction]]:
! i must be one of "orig.ident", "nCount_RNA", "nFeature_RNA", "Patient.Condition", "Patient.Diagnosis", "Patient.ID",
"Patient.Tissue", "Patient.Diagnosis.Tissue", "Patient.Condition.Tissue", "percent.mt", "nCount_SCT", "nFeature_SCT",
"integrated_snn_res.0.6", "seurat_clusters", or "regroup", not "tsne".
Backtrace:
▆
- └─ClusterMap::cluster_map(...)
- └─base::lapply(...)
-
└─ClusterMap (local) FUN(X[[i]], ...) -
└─ClusterMap::recolor_s(da, single_obj_list[[n]], n, reduction = reduction) -
└─Seurat::DimPlot(...) -
├─cells %||% ... -
├─SeuratObject::Cells(x = object, assay = DefaultAssay(object = object[[reduction]])) -
├─SeuratObject:::Cells.Seurat(x = object, assay = DefaultAssay(object = object[[reduction]])) -
│ └─assay[1L] %||% DefaultAssay(object = x) -
├─SeuratObject::DefaultAssay(object = object[[reduction]]) -
├─object[[reduction]] -
└─SeuratObject:::`[[.Seurat`(i = reduction)
Run rlang::last_trace(drop = FALSE) to see 9 hidden frames.
Can you help me in fixing this? Note that my original seurat objects have umap as the reduction method, not t-sne. Can that be a problem? Although, here, something else seems to be the problem. In cluster_map, how do I set "i" to one of the meta data options as the error message suggests? And which meta-data should "i" be set to?
Looking forward to your response! Thanks so much!
Ankita