Elizabeth Purdom

plotHeatmap breaks when sampleData is ordered factor

2

I opened this as separate issue (submitted by @allonw); was previously combined with another issue. When one of the sampleData metadata has spaces, plotHeatmap breaks with an error that doesn't...

Need to add some character valued defaults for distance function

Would be nice in mergeClusters to be able to do plotType=c("adjP","locfdr") i.e. do more than 1 but not all

Need to set up seed option for subsampleClustering when parallelized (ncores>1). But don't want to subsample the same set over and over! Perhaps use seed to pick random integers to...

To allow for weights from zero-inflated, for example.

e.g. if you want to make your own 'clusterMany' more efficiently

plotSilhouette

1

Calculate and plot silhouette values for the clusters using the cluster package functions.

May have been done already, but it was written as a to do in code.

When running combineMany, coClustering doesn't represent proportion of -1 that go into the determination of making clustering. Perhaps try to add this somehow.