Question

plotUMAP and ggplotly Cell IDs Display

0

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Dario Strbenac ★ 1.5k

@dario-strbenac-5916

Last seen 3 hours ago

Australia

How should plotUMAP be used to retain cell IDs so that ggplotly(someUMAP) will show IDs on hover? I have made a faceted UMAP plot, faceted by cell types and some clusters are completely overlapping and not seen to have different cell types in them unless they are faceted. So, I would like to get cell IDs of some cells from cancer facet and cell IDs from fibroblast facet to examine the known marker genes for cancer and fibroblasts of the cells with different cell type but overlapping almost perfectly in UMAP. I have tried using iSEE but found it clunky and was unsuccessful for this task, so am hoping for a lightweight approach to work.

scater • 538 views

ADD COMMENT • link updated 10 months ago by alan.ocallaghan ▴ 160 • written 10 months ago by Dario Strbenac ★ 1.5k

1

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You could at some point add extra geoms to a plot into ggplotly that would show up in the hovertext, eg a text geom to ggplotly that will come up in the hovertext. So something like:

library("scater")

sce <- mockSCE()

sce <- logNormCounts(sce)
sce <- runUMAP(sce)
sce$Cell_name <- colnames(sce)

ggplotly(ggcells(sce) + geom_point(aes(UMAP.1, UMAP.2, text=Cell_name)) + facet_wrap(~Cell_Cycle))

ADD REPLY • link 10 months ago alan.ocallaghan ▴ 160