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How do you plot one slice of a multi-slice spatial dataset? #5774

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royfrancis opened this issue Mar 23, 2022 · 4 comments
Closed

How do you plot one slice of a multi-slice spatial dataset? #5774

royfrancis opened this issue Mar 23, 2022 · 4 comments
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bug Something isn't working

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@royfrancis
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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)

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
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#>  date     2022-03-23
#>  pandoc   2.14.0.3 @ /usr/lib/rstudio/bin/pandoc/ (via rmarkdown)
#> 
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#> ──────────────────────────────────────────────────────────────────────────────
@royfrancis royfrancis added the bug Something isn't working label Mar 23, 2022
@royfrancis royfrancis changed the title How do you plot one slide of a multi-slice spatial dataset? How do you plot one slice of a multi-slice spatial dataset? Mar 23, 2022
@andrewwbutler
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Hi,

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

SpatialDimPlot(brain, images = "anterior1")

@royfrancis
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royfrancis commented Mar 26, 2022 •
edited
Loading

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
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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
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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.

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