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Error in cluster_map - Error in object[[reduction]] #20

@RandomRipples

Description

@RandomRipples

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:

  1. └─ClusterMap::cluster_map(...)
  2. └─base::lapply(...)
  3. └─ClusterMap (local) FUN(X[[i]], ...)
    
  4.   └─ClusterMap::recolor_s(da, single_obj_list[[n]], n, reduction = reduction)
    
  5.     └─Seurat::DimPlot(...)
    
  6.       ├─cells %||% ...
    
  7.       ├─SeuratObject::Cells(x = object, assay = DefaultAssay(object = object[[reduction]]))
    
  8.       ├─SeuratObject:::Cells.Seurat(x = object, assay = DefaultAssay(object = object[[reduction]]))
    
  9.       │ └─assay[1L] %||% DefaultAssay(object = x)
    
  10.       ├─SeuratObject::DefaultAssay(object = object[[reduction]])
    
  11.       ├─object[[reduction]]
    
  12.       └─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

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