Multiple UMAPs

[rasing02]

Hello All,
I have ten groups in the scRNA study, and I want to know if there is a way to obtain the UMAP output for each group in a different PDF file.

The code pasted below outputs all ten groups as one file
pdf("UMAP_group.pdf", width= 46 , height= 18)
DimPlot(seurat.obj, reduction = "umap", split.by= "group", label = FALSE, ncol = 5, raster=FALSE)
dev.off()

I tried setting combine = FALSE to obtain separate pdf's for each group, however this did not work. Please let me know if you have any suggestions.

Thank you!

[samuel-marsh]

Hi,

The issue is not with combine but with the pdf() call which will create on pdf for each call until dev.off().

If you want to create multiple PDFs you can write things as for loop or using apply. To save some time though you can use iterative plotting functions from my package scCustomize (https://samuel-marsh.github.io/scCustomize/articles/Iterative_Plotting.html). See Iterate_DimPlot_bySample.

by sample is really just any meta.data column you choose so in your case above set sample_column = “group”

Best,
Sam

[rasing02]

Thank you Samuel

[rasing02]

Dimplot function works but Iterate is not. I used the following code, but it leads to empty files. It creates an x and y axis for UMAP.
Iterate_DimPlot_bySample(
seuraobj,
sample_column = "group",
file_path = "plots/",
file_name = "umap",
file_type = ".jpeg",
#single_pdf = FALSE,
#color = "black",
dpi = 600,
no_legend = TRUE,
title_prefix = NULL,
reduction = "umap",
#pt.size = NULL,
#raster = NULL,

)

[samuel-marsh]

Can you post to scCustomize repo so I can better track and help with this?

thanks,
Sam

[rasing02]

I just posted to scCustomize repo. Thank you!