Elizabeth Purdom

If the input to `annCol` or `annRow` is a ordered factor, `aheatmap` creates an error. Here is example code: aaa = matrix(runif(100), nrow = 10) anno = factor(sample.int(3, size =...

Create a `minSizes` argument for merging, so that the algorithm just always merges a cluster in if its less than a certain size. It might also speed up the DE...

And make sure matches dendro if `contrastType="Dendro"`

Also a plotting function. If one cluster, then pairwise between clusters. If two clusters then correlations between pairs of their clusters. Names: `clusterCor` and `plotClusterCor`

This code has basically already been written in clusterManyTest.R -- just needs to be converted into proper function. Also a function to change the internal ids so that if they...

Store counts as integers

2

to save space.

Need to figure out what violin plot package is best...

`plotDendrogram` is *much slower* than `plotClusters`, probably having to do with the fact that it calls the ape function for plotting the rectangles, and done individually per cell. Not really...