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Following sc-type quick guide tutorial at https://github.com/IanevskiAleksandr/sc-type, I am having an issue with bubble plot visualization to show cell types for cluster annotation:

scater::multiplot(DimPlot(ddata_3tf, reduction = "umap", repel = TRUE, 
  label = TRUE, cols = ccolss), gggr, cols = 2)

error returned in bubble plot viz of multiplot being defunct:

Error: 'multiplot' is defunct.
Use 'scater::multiplot is defunct.
Use 'gridExtra::grid.arrange' instead' instead. See help("Defunct")

How would I properly incorporate scater::multiplot() parameters into gridExtra::grid.arrange()?

Trying

gridExtra::grid.arrange(DimPlot(ddata_3tf, reduction = "umap", repel = TRUE, 
  label = TRUE, cols = ccolss), gggr, cols = 2)

returns

Error in gList(...) : only 'grobs' allowed in "gList"

Here is the error traceback too:

14. stop("only 'grobs' allowed in \"gList\"")
13. gList(...)
12. setChildren(gt, children)
11. gTree(children = gList(...), name = name, gp = gp, vp = vp, childrenvp = childrenvp, cl = cl)
10. grobTree(grob, name = vp$name, vp = vp)
9. (function (grob, vp) { grobTree(grob, name = vp$name, vp = vp) })(dots[[1L]][[3L]], dots[[2L]][[3L]])
8. mapply(wrap_gtableChild, x$grobs, children_vps, SIMPLIFY = FALSE)
7. makeContent.gtable(x)
6. makeContent(x)
5. drawGTree(x)
4. recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
3. grid.draw.gTree(g)
2. grid.draw(g)
1. gridExtra::grid.arrange(DimPlot(ddata_3tf, reduction = "umap", repel = TRUE, label = TRUE, cols = ccolss), gggr, cols = 2)

Trying

gridExtra::grid.arrange(DimPlot(ddata_3tf, reduction = "umap", repel = TRUE, 
  label = TRUE, cols = ccolss), gggr, cols = 2)

returns

Error in gList(...) : only 'grobs' allowed in "gList"
MrFlick
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Pcrucifer
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  • Have you tried it without the `cols` parameter? It looks like in `gridExtra::grid.arrange()` the corresponding parameter is `ncol`. See here: [https://stackoverflow.com/questions/34838870/grid-arrange-from-gridextras-exiting-with-only-grobs-allowed-in-glist-afte](https://stackoverflow.com/questions/34838870/grid-arrange-from-gridextras-exiting-with-only-grobs-allowed-in-glist-afte) – Cloudberry Jun 29 '23 at 20:06

0 Answers0