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I would like to know how to change the UMAP used in Dimplot and FeaturePlot from Seurat: how we can get the x-axis and the y-axis like UMAP-1 and UMAP-2 if I want to use UMAP-4 and UMAP-5. How to modify the code? It is easy to change the PC by using DimPlot(object = pbmc_small, dims = c(4, 5), reduction = "PCA") but if I changed to reduction = "UMAP", I got the error 

"Error in Embeddings(object = object[[reduction]])[cells, dims] : subscript out of bounds Calls: DimPlot Execution halted".

Does anyone have any idea how to solve this problem?

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    $\begingroup$ that is because UMAP-4 and UMAP-5 are not present in your object...head(object[['umap']]@cell.embeddings), or str(object[['umap']]@cell.embeddings) $\endgroup$
    – Mack123456
    Commented Dec 23, 2019 at 23:37
  • $\begingroup$ Yes, the UMAP-4 and UMAP-5 are not present in my project. So what should I do now? $\endgroup$
    – hua
    Commented Dec 24, 2019 at 2:41
  • $\begingroup$ What is the rationale for using UMAP-4 and UMAP-5? UMAP is different from PCA because you specify a dimension (usually) and it tries to put all information in those two dimensions. $\endgroup$
    – Phoenix Mu
    Commented May 14, 2020 at 13:42

2 Answers 2

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Try this:

library(Seurat)
pbmc_small <- RunUMAP(pbmc_small, dims = 1:10, reduction = "pca", n.components = 5)

names(pbmc_small[["umap"]])
#> [1] "UMAP_1" "UMAP_2" "UMAP_3" "UMAP_4" "UMAP_5"

# plot
DimPlot(pbmc_small, reduction = "umap", dims = c(4, 5))

enter image description here

This should work with Seurat version 3.1.5

packageVersion("Seurat")
#> [1] '3.1.5'
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Change n.components / max.dims (depending on your seurat version) to 5 when you call runUMAP and you should have dim 4 and 5 available.

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  • $\begingroup$ Hi Pallie, i have tried to use "SAN <- RunUMAP(SAN, dims = 1:10, max.dim = 5L, dims.keep = 5L)" and there still are no UMAP-4 and UMAP-5. $\endgroup$
    – hua
    Commented Dec 24, 2019 at 15:48

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