CODEWITHSUNDEEP
rdata-analysisbioconductorcatalyst
Jamie Tian
Jamie Tian

Reputation: 1

catalyst package plot MST

I'm just wondering how to plot a MST, just like when using flowsom, but do it using the catalyst package instead. I have followed the catalyst tutorial on bioconductor and just finished the clustering bit. It would be nice to be able to visualise the clustering using a MST but I am not sure how to do it... Thanks a lot for helping

Here's the code I tried for clustering using catalyst package:

sce <- cluster(sce, features = "type", 
               xdim = 10, ydim = 10, maxK = 20, 
               verbose = FALSE, seed = 1)

Then I tried the following to plot a MST:

fsom <- metadata(sce)$SOM
PlotStars(fsom, view = "MST", backgroundValues = fsom$metaclustering)

However I got the following: Error in UpdateFlowSOM(fsom) : fsom should be a FlowSOM object.

I'm not sure how to make this work now...

Upvotes: 0

Views: 34

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