Jamie Morton

Adding alternative ordination and clustering methods

19

Looking at Visumap, the majority of those algorithms are found in scikit-learn or scikit-bio, namely **Ordination** - [SMACOF](https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/manifold/mds.py) - [Correspondence Analysis](https://github.com/biocore/scikit-bio/blob/master/skbio/stats/ordination/_canonical_correspondence_analysis.py) **Classification** - [Linear Discriminate Analysis](https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/lda.py) - [Nearest Neighbor](https://github.com/scikit-learn/scikit-learn/tree/master/sklearn/neighbors) **Clustering**...

Adding in kernel density estimation

7

One thing that I think could potentially really clarify the the PCoA plots is to have some kernel density estimators. This could not only allow the user to visualize where...

Adding midpoint coloring

1

It would be great if there was support for diverging colormaps (vmin, vcenter and vmax) as done in matplotlib's [TwoSlopeNorm](https://matplotlib.org/stable/api/_as_gen/matplotlib.colors.TwoSlopeNorm.html#matplotlib.colors.TwoSlopeNorm). I think this use-case will become increasing common for publishing...

Paired heatmaps

1

It would be really cool if there was a paired heatmap interface in calour. This would be especially useful for linking paired omics datasets. We have a PR here: https://github.com/biocore/rhapsody/pull/75...

download button appears to be broken

4

It looks like the save functionality is having some issues on my install. I can't seem to download the png via the save button - is this expected? 

Robust quantiles

5

Would be nice if the heatmap colors were scaled to robust quantiles rather than the extreme values See seaborn robust parameter http://seaborn.pydata.org/generated/seaborn.heatmap.html

Change `sample_color_bars` to `sample_highlights`?

2

I feel that people will mix up the heatmap colorbars with the box indicating sample and feature categories. What do you guys think about changing this parameter name to `sample_highlights`...

Would be nice if the highlights could handle continuously valued categories (i.e. pH)

Would you guys be interested in incorporating niche_sort? https://github.com/biocore/gneiss/blob/master/gneiss/sort.py#L91 In my experience, this has been incredibly useful for 1. Sorting bacteria along a gradient 2. Sorting bacteria by how associated...

missing a space.