Labeling Clusters in ggplot
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4 months ago
fouerghi20 ▴ 30

I have a data matrix I extracted from seurat and I want to plot the tSNE plot by using ggplot. I don't know how to label the clusters on the plot with 0..15. Help is appreciated.

ggplot single cell • 376 views
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You have to show sample input data. Also, please show what you have already tried.

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Why do you want to plot the t-SNE outside from seurat? As far as I know seurat uses ggplot2 package, meaning that you can add layers to the plot in the same way you do in ggplot2.

Therefore my question is: what do you expect to plot in ggplot2 that the seurat can't do (since it uses ggplot2)?

With this I don't mean that there is not advantages of using ggplot2 instead of using it with the seurat functions interface, but I'm just curious...

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Agreed. If you just want more viz options and some convenience, you could also consider dittoSeq.

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3 months ago
fouerghi20 ▴ 30

This is what ended up working for me:

data$seurat_clusters <- factor(data$seurat_clusters,labels=c("..",".."))

data2 <- data %>% group_by(seurat_clusters) %>% select(tSNE_1, tSNE_2) %>% summarize_all(mean)
View(data$seurat_clusters)

ggplot(data, aes(tSNE_1,tSNE_2, col = factor(seurat_clusters, labels= c("..",".."))),label= TRUE)+ geom_point(size=0.3,alpha=0.3) +   labs(color= "Clusters") +  ggrepel::geom_label_repel(data = data2,aes(label = seurat_clusters))
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