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Help with setting DimPlot UMAP output into a 2x3 grid in Seurat

Bioinformatics Asked on October 3, 2021

On my merged seurat object of 6 samples, when I use the split.by function in tandem with the Dimplot/UMAP plot, all six samples are displayed in series along a commonly labeled ‘UMAP_1’ x-axis in an order of (these are arbitrary for simplicity, here) Z, Y, X, C, B, A. Instead, I would like to specify these plots to output as a 2 row x 3 column arrangement ordered (1st Row) A, B, C and (2nd Row) X, Y, Z.

I’m assuming I could use something like: group_levels <- c("A", "B", "C", "X", "Y", "Z") to define the order I’d like, but I’m lost on how to get this to arrange the UMAP plots into a 2×3 grid I’d like.

Appreciate any help!

One Answer

how to get this to arrange the UMAP plots into a 2x3 grid

You can use the ncol parameter, which will set the number of columns in the "combined plot".

And for future reference, if you get the help page of the function you are using with ?DimPlot, you will see the .... This means that you can feed additional arguments to other functions that DimPlot() uses. Apparently, CombinePlots() is used under the hood and has an ncol parameter.

Correct answer by haci on October 3, 2021

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