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This #29 works but it needs a front end for the user and a display page.

Add alpha plots for stddev stderror

Currently, the left menu is only a visualization aid but it will be better if the user could select the fields to use for further analyses.

When the categories of a column in the mapping file has no alphanumeric characters (for example '), the coloring by metadata doesn't work.

Export plot as svg image

https://github.com/qiime/evident/blob/master/evident/rarefaction.py#L20

As discussed in #44, the Emperor source files should be hosted as a git submodule.

Ideally:

pip install numpy
pip install evident

When rotating a PCoA plot and trying to use the Recenter Camera button in the Options tab, the camera is not completely re-centered.

It was mentioned that this issue could be caused given a bug in Three.

@antgonza and I decided that Evident should have it's own Makefile such that the system could be deployed in any host and get you a working version of Evident.

Much better to have users interact directly with Qiita or have commands to download data

Currently the project works only with unweighted unifrac but the engine is designed to run with any beta metric. I think weighted and unweighted unifrac should suffice, what do you think? If we decide to go with all metrics I believe the demo version should only work with we/un unifrac.

The python code that writes the HTML document in Evident is now being implemented in a more cohesive manner in qiime/emperor. Once Emperor, reaches a more stable state on it's own, E-vident should take advantage of it.

This should probably be a git submodule inside E-vident.

Add a slider in the options that controls the radius of the balls

Create histograms for fraction of the time that we will see that separation

Currently you can click on a label in the key and it will locate the ball, add functionality to do the opposite.

Add labels to PCoA axes

There are a couple errors that show up in the JavaScript console when loading the front page of Evident; most of these are PNG files.

To reproduce this issue, just open front page and look at the JavaScript console.

Add how many samples are in each category. Currently there is no easy way to see how many samples are under each category: Control/Fast

Add test code

Google docs install instructions for evident need to be converted to online install documents.

On #25 we found an odd behavior when plotting on parallel stderr and stddev: one is taking longer than the other and we do not know why? We need to figure out if this is a problem with qiime, expected behavior or something else.

Figure out a way to select a group of samples that should always be used for the random selection of samples, an easy way can be by metadata. This feature will be useful for temporal or any other gradient studies, as you could set that always selected group as those from time 0, then the controllers will only allow you to select parameters between those samples and you can run your calculations.

Make sure that the 3d ellipses are correct

Some updates to evident/pcoa.py and evident/evident.py were merged without an update to their respective tests modules. Running test_pcoa.py and test_evident.py fail.

Currently, everything runs single core but we should allow, maybe via a config file, to run in parallel both alpha and beta.

Use same rarefactions for alpha both errors

Matplotlib requires a tmp folder to be set properly. Currently, Evident is using a random temporal folder but it should be using the one from the qiime configuration.

When installing the Virtual instance of Evident and open up the link in Chrome, none of the data is shown and none of the bars work. A screenshot is shown below.

The text that describes the available studies is not updated to reflect the latest changes.