clustree producing clustering trees using ggraph Luke Zappia @_lazappi_ lazappi.github.io/clustree

My data OpenStax College, CC BY 3.0 via Wikimedia Commons Single-cell RNA-sequencing Gene activity in thousands of cells ~20000 features (genes) ~8000 samples (cells) Look for different cell types

How many clusters?

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Sample K1 K2 K3 0 A A A 1 A B C 2 A A A 3 A A B 4 A B A 5 A A B 6 A B C 7 A A A 8 A A B 9 A B C

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How do we do that in R?

Clusters + transitions ID Resolution Cluster Size 1A 1 A 10 2A 2 A 6 2B 2 B 4 3A 3 A 4 3B 3 B 3 3C 3 C 3 From To Number 1A 2A 6 1A 2B 4 2A 3A 3 2A 3B 3 2B 3A 1 2B 3C 3

ggplot?

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Building a graph igraph::from_data_frame(edges, vertices = nodes) tidygraph::tbl_graph(edges, nodes) graph %>% activate(nodes) %>% filter(...) %>% mutate(...) %>% activate(edges) %>% filter(...) %>% mutate(...)

ggraph ggraph(graph, layout = “tree”) + geom_edge_link(...) + geom_node_point(...) + scale_size(...) + scale_edge_colour(...)

clustree(clusterings, ...)

What does it look like?

Simulations - 1 group

Simulations - 4 groups

The Iris dataset Tiia Monto CC BY-SA 4.0, via Wikimedia Commons C T Johansson CC BY 3.0, via Wikimedia Commons Jefficus, via Wikimedia Commons Iris setosa Iris versicolor Iris virginica

Iris dataset k-means clustering k = 1,...,5

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Petal length

Organoid data

NPHS1

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t-SNE 2 t-SNE 1 t-SNE 1 t-SNE 2

Acknowledgements Everyone that makes tools and data available MCRI Bioinformatics Belinda Phipson MCRI KDDR Alex Combes @_lazappi_ lazappi.github.io/clustree install.packages(“clustree”) Paper doi.org/10.1101/274035 Slides tinyurl.com/clustree-useR2018 Supervisors Alicia Oshlack Melissa Little