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NelleV / moanin

Timecourse transcriptomic analysis
https://nellev.github.io/moanin/
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Undefined variable in splines_kmeans_score_and_label #29

Closed epurdom closed 4 years ago

epurdom commented 4 years ago

There appears to be a variable meta in splines_kmeans_score_and_label that is not defined:

I think this is left over from some change in code, but I don't actually see how to fix it, since the user doesn't pass a moanin_model object...

splines_kmeans_score_and_label = function(data, kmeans_clusters, percentage_genes_to_label=0.5,
                      max_score=NULL,
                      rescale_separately_on=NULL){

    n_clusters = dim(kmeans_clusters$centroids)[1]
    all_scores = matrix(NA, nrow=dim(data)[1], ncol=n_clusters)

    if(!is.null(rescale_separately_on)){
        groups = levels(meta[, rescale_separately_on]) ###<<<<----- HERE
    }
NelleV commented 4 years ago

That's definitely something from an old API, and also something that we don't currently use in the pipeline. I'm going to fix this, as it is useful to reproduce the results of the EPICON paper.