Elizabeth Purdom
Elizabeth Purdom
This could probably be done by getting the order within each cluster via hclust within cluster, then concatenating the orders to get a single ordering and using the reorder.dendrogram function...
The order idea doesn't work. At least not well, because only will rotate existing left/right. Have to create method to paste the trees together. Much more annoying... Have started some...
Also, now the internal code relies heavily on 0-length edges within a cluster to distinguish cluster nodes and outbranch nodes ... so must be careful not to disrupt that.
Currently added this information to documentation of plotHeatmap telling user to define colors with `clusterLegend` if there are many factors/levels. If fix this problem, should remove this warning.
I missed the error part of this. So I opened the error as a separate issue and adjusted the title.
Because problem with ordered factors in aheatmap (#184) have not added this yet as enhancement.
Is there any chance this can be related to the graphics device? plotHeatmap is very finicky if there is an interruption of plotHeatmap (e.g. an error). Often if aheatmap was...
Problem is that dimensionality reduction is done BEFORE giving param Matrix to the most basic version. Need to read paramMatrix and figure out dimReduce parameters... And, column of paramMatrix does...
This also has some urgency because vignette talks about doing this, but it doesn't work. Might need to delete out of vignette for now and some back to this.
For now, remove functionality and comment out in vignette.