Reorder ClusterTree

[annaliem]

Is there a way to reorder the cluster tree in PlotClusterTree to the original cluster order?

BuildClusterTree(SO, slot = "scale.data")
PlotClusterTree(SO, direction = "rightwards")

Looking to have the tree ordered as OT1, OT2, OT3, OT4, etc. so I can stick it next to a dot plot. Using Seurat 4.0.3.

[AmelZulji]

Hi @annaliem,

One way to have "synchronized" dotplot and clustertree is to reorder identities based on the clustertree:
SO <– BuildClusterTree(SO, slot = "scale.data", reorder = T)
Then order of identities in you object will match order of clustertree plot and you can merge both plots.

hope it helps,
Amel

[annaliem]

Hi Amel,

Thank you for your response! Unfortunately I have tried that and I only see reordering of one or two clusters. I apologize - I should have included that in my initial post.

BuildClusterTree(SO, slot = "scale.data", assay = "SCT", reorder = T)
tree <- Tool(object = SO, slot = "BuildClusterTree")
ape::plot.phylo(x = tree, direction = "rightwards")

Note: I used ape::plot.phylo to plot without nodes, but ordering between that and PlotClusterTree is identical.

[AmelZulji]

Hi @annaliem,
One possible reason that you are seeing unexpected results is because you are not assigning the built tree to the object. Instead of this:
BuildClusterTree(SO, slot = "scale.data", assay = "SCT", reorder = T)

you should be doing this:
SO <- BuildClusterTree(SO, slot = "scale.data", assay = "SCT", reorder = T)

Using pbmc_small object provided within Seurat package, this is how it should look like:

library(Seurat)

# Rename clusters randomly
pbmc_small <- RenameIdents(pbmc_small, 
                           "2" = "cluster1",
                           "0" = "cluster2",
                           "1" = "cluster3")

# Build cluster tree without reordering
pbmc_small <- BuildClusterTree(pbmc_small)
tree <- Tool(object = pbmc_small, slot = "BuildClusterTree")
ape::plot.phylo(x = tree, direction = "rightwards")

If you plot the dotplot, the order of clusters in dotplot does not match the order of clusters in the tree

# Plot some random genes
DotPlot(pbmc_small, features = c("MS4A1", "CCL4"))

However, if you build the tree with reordering then the orders of cluster in dotplot will match the order from the tree:

pbmc_small <- BuildClusterTree(pbmc_small, reorder = T)
DotPlot(pbmc_small, features = c("MS4A1", "CCL4"))

Then you can you can plot those 2 plots side by side and the order will match.

Hope it helps.

BEst,
Amel