Using clustree with CATALYST::cluster() output

[antoine4ucsd]

Hello I am working on flow data and I am trying to plot the resulting cluster tree from the output: sce <- CATALYST::cluster(sce, features = "type", xdim = 20, ydim = 20, maxK = 140, seed = 1234) sce class: SingleCellExperiment dim: 9 42990473 metadata(4): experiment_info cluster_codes SOM_codes delta_area assays(2): counts exprs rownames(9): PD-1 CD3 ... CD8 CD4 rowData names(4): channel_name marker_name marker_class used_for_clustering colnames: NULL colData names(4): sample_id condition patient_id cluster_id reducedDimNames(0): altExpNames(0):

I can't figure out how to run clusttree (prefix?) all ideas are welcome

thanks much!

[lazappi]

Hi @antoine4ucsd

I'm not familiar with the CATALYST::cluster() function so I don't know what it returns but to use clustree you will need a series of columns in colData(sce) that contain the clustering labels for each resolution you want to plot. These should be named something like "prefixX" where "prefix" is the same for all columns and "X" gives the resolution. You can then call the clustree() function like clustree(sce, prefix = "prefix_", ...).

Hope that helps 😸

[antoine4ucsd]

Thank you

a

On Dec 11, 2020, at 12:37 AM, Luke Zappia notifications@github.com wrote:

 Hi @antoine4ucsd

I'm not familiar with the CATALYST::cluster() function so I don't know what it returns but to use clustree you will need a series of columns in colData(sce) that contain the clustering labels for each resolution you want to plot. These should be named something like "prefixX" where "prefix" is the same for all columns and "X" gives the resolution. You can then call the clustree() function like clustree(sce, prefix = "prefix_", ...).

Hope that helps 😸

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