cloupe file to Loupe Brower8.0 get a different plot

[jiangldu]

hello, when importing cloupe file to Loupe Brower8.0 , i got a different plot comparing with dimplot(). In Loupe Brower, when seting "split view", it would get a very scattered plot. use FindIntegrationAnchors() and IntegrateData() functions to merge 10xgenomic datasets. use create_loupe() to get cloupe file , the commands as. create_loupe(count_mat = GSE165318.combined@assays$RNA$counts, clusters = clusters, projections = projections, output_dir = "./", output_name = "GSE165318.combined.1", seurat_obj_version = "Seurat4") DimPlot(GSE165318.combined,reduction = "tsne",group.by = "seurat_clusters") DimPlot(GSE165318.combined,reduction = "tsne",group.by = "seurat_clusters", split.by = "celltype")

ls(projections) [1] "tsne" "umap" ls(clusters) [1] "active_cluster" "celltype" "GSE.Group"
[4] "GSE.Sample" "integrated_snn_res.0.5" "orig.ident"
[7] "Row.names" "seurat_clusters"

plots in Loupe Brower:

[gmjoseph]

hi @jiangldu thanks for filling this issue - could you also share the result of dimplot() please? thank you.

[jiangldu]

dimplot :