tutorials

[andrewheusser]

To help users get started with the tutorial, it would be nice to have a set of tutorials that go over the main features (something like this: http://cdl-quail.readthedocs.io/en/latest/tutorial.html). Each tutorial can be a separate Jupyter notebook.

• Notebook titles should written in a markdown cell using # to make it large
• Subtitles should be written in a markdown cell using ## to make them a bit smaller
• Descriptions should be written in a markdown cell with no pound sign

• Code examples should in in python

  See here for an example of how to format as described above.

Here is what I'm thinking. Please check these off as you go so we can keep track, and if you run into any issues, leave a message on this thread and move on to the next thing.

1. A notebook highlighting the hyp.plot function - examples of:

• [x] importing the toolbox
• [x] loading in some example data i.e. mushrooms
• [x] plotting with defaults i.e. geo = hyp.plot(data, '.')
• [x] plotting in 2D (setting ndims=2)
• [x] plotting with different dimensionality reduction (TSNE)
• [x] plotting with grouping (setting group=list_of_group_labels)
• [x] plotting with labels (labelling a subset of points to labels)
• [x] plotting with a legend (setting legend=True)
• [x] interpolating missing data (set some of the points to nan)
• [x] plotting with clusters (setting n_clusters)
• [x] plotting with normalization (setting normalize='within')
• [x] plotting with alignment (example)
• [x] saving a plot (save_path=something)

2. A notebook highlighting the hyp.analyze function. examples of:

• [x] importing the toolbox
• [x] loading in some example data i.e. weights_avg
• [x] an example normalizing the data
• [x] normalizing + reducing
• [x] normalizing + reducing + aligning

3. A notebook highlighting hyp.normalize examples of:

   • [x] importing the toolbox
   • [x] generate some synthetic data (see this example)
   • [x] normalize within
   • [x] normalizing across
   • [x] normalizing by row

4. A notebook highlighting dimensionality reduction with hyp.reduce. examples of:

• [x] importing the toolbox
• [x] loading in some example data i.e. mushrooms
• [x] reducing a single array
• [x] reducing a list of arrays
• [x] reducing a list of arrays with TSNE
• [x] reducing a list of arrays where ndims>3
• [x] reducing a list of arrays and tweaking the model parameters using the dictionary syntax

5. A notebook highlighting hyp.align. examples of:

• [x] importing the toolbox
• [x] loading in some example data i.e. weights
• [x] plotting two unaligned datasets (using the line plot not '.')
• [x] plotting two aligned datasets aligned with hyperalignment
• [x] plotting two aligned datasets aligned with SRM

6. A notebook highlighting hyp.cluster examples of:

• [x] importing the toolbox
• [x] loading in some example data i.e. mushrooms
• [x] return cluster labels with default args
• [x] setting n_clusters equal to something other than the default
• [x] using a different cluster model e.g. cluster='AgglomerativeClustering'

7. A notebook highlighting the geo class. examples of:

• [x] importing the toolbox
• [x] loading in some example data i.e. mushrooms
• [x] plot the data and generate a geo
• [x] description of each of the fields (see here for API description)
• [x] using geo.plot
• [x] transforming new data geo.transform(new_data)
• [x] saving data with geo.save

[jeremymanning]

Sounds like a great idea! :+1:

These should probably go into this repo, and we should consider renaming that repository to hypertools-examples or simililar (and then we should update all links to the original notebook).

The reason to include these in a separate repo is to prevent users/developers from having to download extra stuff if they just want to work on the code. (But they are also small files...so I'm open to alternative ideas and/or including them in this repo if there's a compelling reason.)

[andrewheusser]

For quail, I have these in the docs folder, because you can autocompile notebooks into a website see here.

[jeremymanning]

That looks perfect-- let's do that!

[andrewheusser]

I've finished and push edits on 4/7 tutorials. Will finish the rest today/tomorrow!