search

satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
Other
2.19k stars 891 forks source link

ImageDimPlot - how *not* to show the clusters data in Xenium object #8471

Open hannalab opened 4 months ago

hannalab commented 4 months ago

Hey, I have a Seurat object from Xenium data, and I clustered the scRNA-seq, so I have seurat_clusters in the object now. I want to use ImageDimPlot(), but not to plot the ident colors, only the molecules. How can I do it? Thanks!

dcollins15 commented 4 months ago

You should be able to color by any column in the object's meta.data slot by setting the group.by parameter - let us know if you're still running into any issues 🙂

yxue88 commented 3 weeks ago

hello, is your seurat object from integreated objects? have you figured out this issue? thank you!