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Use scaled fitted values for DMM drivers #881

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Use scaled fitted values for DMM drivers #881

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8 changes: 5 additions & 3 deletions inst/pages/clustering.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -304,11 +304,13 @@ features.
#| fig-height: 2

# Get the estimates on how much each phylum contributes on each cluster
best_model <- metadata(altExp(tse, "prevalent"))$DMM$dmm[2]
drivers <- as.data.frame(best_model[[1]]@fit$Estimate)
models <- metadata(altExp(tse, "prevalent"))$DMM
n_clusters <- models[["best"]]
best_model <- models[["dmm"]][[n_clusters]]
drivers <- fitted(best_model, scale = TRUE)

# Plot by utilizing miaViz's function plotLoadings
plotLoadings(as.matrix(drivers), ncomponents = 2)
plotLoadings(drivers, ncomponents = 2)
```

As well as in hierarchical clustering, we can also visualize the clusters by
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