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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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How do you plot one slice of a multi-slice spatial dataset? #5774

Closed royfrancis closed 2 years ago

royfrancis commented 2 years ago 
library(Seurat)
#> Attaching SeuratObject
library(SeuratData)
#> ── Installed datasets ───────────────────────────────────── SeuratData v0.2.1 ──
#> ✓ stxBrain 0.1.1
#> ────────────────────────────────────── Key ─────────────────────────────────────
#> ✓ Dataset loaded successfully
#> > Dataset built with a newer version of Seurat than installed
#> ❓ Unknown version of Seurat installed

brain1 <- LoadData("stxBrain", type = "anterior1")
brain2 <- LoadData("stxBrain", type = "posterior1")
brain <- merge(brain1, brain2)
#> Warning in CheckDuplicateCellNames(object.list = objects): Some cell names are
#> duplicated across objects provided. Renaming to enforce unique cell names.

SpatialDimPlot(brain)

SpatialDimPlot(subset(brain,subset=region=="anterior"))

SpatialDimPlot(subset(brain,idents="anterior1"))

Created on 2022-03-23 by the reprex package (v2.0.1)

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andrewwbutler commented 2 years ago

Hi,

You can specify the image parameter to plot a single slice. E.g.

SpatialDimPlot(brain, images = "anterior1")
royfrancis commented 2 years ago

This didn't initially work for me due to #5128. Then I removed the package SpatialExperiment, restarted and then it worked. But, one minor issue is that the legend is still incorrect showing slices that are not displayed.

SpatialDimPlot(brain, images = "anterior1")

e

In addition, I don't think the ncol argument works.

SpatialDimPlot(brain,ncol=1)

andrewwbutler commented 2 years ago

The legend issue should be fixed now on the latest develop branch (v4.1.0.9002). ncol is a bit more complicated. For now, I'd recommend passing combine = FALSE to get a list of plots and then combining in your preferred arrangement using something like patchwork::wrap_plots().

andrewwbutler commented 2 years ago

The ncol should now work properly on the latest develop branch (v4.1.0.9005). Thanks for the reprex and please reopen if issues persists.