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SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
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Functions in the previous SingleR version (SingleR1.0) #124

Closed Sa753 closed 4 years ago

Sa753 commented 4 years ago

Hi Aaron,

There were quite nice functions in the previous version of SingleR in 2019 especially related to plotting heat maps and TSNE/UMAP on Seurat clusters. Unfortunately, when I tried using any of those functions, I can't find them anymore.

Is there anyway to restore that please?

Thanks

j-andrews7 commented 4 years ago

The vignette and manual show how you can create heatmaps from the results, see ?plotScoreHeatmap. The README shows how you can add results back to your Seurat objects, at which point they can be plotted like any other metadata variable:

seurat.obj[["SingleR.labels"]] <- singler.results$labels

# Or if `method="cluster"` was used:
seurat.obj[["SingleR.cluster.labels"]] <- 
        singler.results$labels[match(seurat.obj[[]][["my.input.clusters"]], 
               rownames(singler.results))]
Sa753 commented 4 years ago

Thank you so much.