0.9.6

Update ChangeLog.md

Emperor 1.0.0: first official beta release

This marks the first beta release of the entire rewrite of Emperor. A lot has changed internally, though most of the user interface and interaction remains the same. For more information about some of the changes, you can watch our SciPy 2016 presentation.

At a glance, Emperor now includes:

• Support for Python 2 and Python 3.
• A new and improved Python and JavaScript API.
• Support to plot Pandas dataframes (see scatterplot).
• Better support for the Jupyter notebook and nbviewer, we have created a few examples for you to try out here and here.
• Improved API-level documentation, while this is still a pre-release the rendered documents will be hosted and updated here: http://emperor.microbio.me/uno/
• Ability to save plot state into a settings file that can later be loaded.
• Among many other interfaces, our command line interface is now provided as a QIIME 2 plugin, see the repository here and information on how to install this plugin and others here.
• Several performance improvements and bug fixes.

Note: This is a pre-release, as there are still several things that will change, and a few features that are still missing. However, we want to make sure that we get your feedback before we consolidate 1.0.0.

To install this pre-release of emperor, you can now use conda or pip:

pip install emperor --pre

conda install -c biocore emperor jupyter

If you want to get involved with development, please see this issue where we are keeping track of the remaining open issues leading to 1.0.

🎉 🐧 🐍

Emperor 0.9.51: stable release.

We are excited to present version 0.9.51 of Emperor! This is a minor update to the 0.9.5 release. You can review our ChangeLog.md for a description of the changes.

Emperor 0.9.5: stable release.

We are excited to present version 0.9.5 of Emperor! Review the change log to see a detailed list of the new features, bug-fixes and maintenance changes.

The user interface to select metadata categories has been enhanced by chosen, this widget makes searching and selecting metadata categories easier and faster.

The continuous coloring checkbox under the Colors tab has been removed, colormaps can now be selected from a single menu, the choices are powered by ColorBrewer2.

Emperor’s official website includes a new section that entirely describes the interface of make_emperor.py, the format of the required files and the python objects available for use with the IPython notebook, go to this link to have a look.

To upgrade to the latest version you will need scikit-bio > 0.2.1 and < 0.3.0 which depends on scipy and a few other scientific python packages, these can get installed using Anaconda or Canopy Express.

Thanks to all the contributors and users that made this release happen.

Emperor 0.9.4: stable release.

We are excited to present version 0.9.4 of Emperor, review the change log to see a detailed list of the new features, bug-fixes and maintenance changes.

Most notably this release adds an Animations tab to the user interface, this new feature aims to provide an easy way to animate a trace using the numerical categories provided in your mapping file. At this point this should be considered an experimental feature that is stable enough to be usable but not on its final form, we need your feedback to make it better. If you are curious this is an example of the kind of animation that inspired this feature and here you can experiment with this feature within Emperor. To animate, go to the Animations tab, then select HOST_SUBJECT_ID in the Trajectory Category drop down menu, then hit play (like in the animated GIF below):

Some of the most important bug-fixes in this release are:

• A problem where users couldn’t scroll through values in the visibility tab (see #235).
• Coordinates files with large values would not be displayed in the user interface (see #233).
• Long category names would be trimmed in the user interface.
• Category names would be sorted incorrectly (see #274)

If you are an IPython notebook user you will be happy to know that we have added a layer of integration for Emperor plots to be displayed inline, see #281

To upgrade to the latest version you will need scikit-bio which depends on scipy and a few other scientific python packages, these can get installed using Anaconda or Canopy Express.

Thanks to all the contributors and users that made this release happen.

Emperor 0.9.1 release.

New features

• Scientific notation is now taken into account in the GUI for scientific coloring.
• GUI is usable in mobile devices that support WebGL.
• User documentation: tutorial, installation instructions, GUI description, etc.
• Ability to make plot comparisons (very useful for procrustes analysis plots).
• The user can select the number of axes to be considered in the GUI and re-plot using lower axes; this is, for example: PC3 vs PC4 vs PC10.
• In missing_custom_axes_values you can reference other column within the mapping file to place the samples without numeric values at different points in the gradient.
• Parallel plots functionality.
• Separated out some options to the View menu.
• The "Colors" tab now has a selector, which allows to use the arrows to move between categories.
• Default coloring scheme is discrete.
• Add color pickers for the axes and axes labels.
• To take a screenshot (PNG) of your current visualization you can press ctrl+p.
• Export to SVG your visualization.
• Emperor now relies on QIIME 1.7.0.
• Added option --number_of_segments to control the quality of all spheres
• Labels for biplots now have a color picker.
• Add color pickers for connecting bars in coordinate comparison plots.
• Add option to select a master set of coordinates when making a comparison plot.
• Adds a feature to negate axes. With this feature you can negate the coordinates of each data point. As a result, the spheres and/or edges will be adjusted appropriately.
• Minor additions to the separator controller for the side bar.
• As of 308629f Emperor is now released under a BSD license.

Bug Fixes

• Fixes recenter camera not working.
• Category names are sorted alphabetically.
• Category names with non-alphanumeric characters are colored correctly now.
• Biplots checkbox now accurately reflects status of biplot visiblity rather than opposite.
• Comparison bars checkbox now accurately reflects status of the visiblity rather than opposite.
• Scaling by percent explained now works with vectors and coordinate comparison plots.
• Fixed bug where only the first bars in coordinate comparison plots could be hidden.
• Improved documentation for saving and exporting images.
• Emperor now fails graciously when WebGL is not enabled and gives you a few suggestions on how to get it to work.