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Emperor ChangeLog

Emperor 1.0

Introducing Emperor 1.0, an improved and new version of Emperor. Including a stable Python API and JavaScript API.

Emperor 0.9.51-dev

Bug Fixes

  • Fix problem where the taxonomic vectors weren't scaled properly when the scale coordinates button was toggled (#386.
  • Fix problem where make_emperor.py would attempt to parse Icon? files when a directory was passed via the -i option (#323).
  • Fix bug where Emperor would try to animate trajectories with a single timepoint i.e. a single unique value in the gradient category.
  • Fix bug where the output saved to --biplot_fp would list the principal coordinate axes starting at zero instead of one (#389).
  • Remove misleading "QIIME version" from index.html (#447).

Miscellaneous

  • Reorganized emperor/support_files/ to separate Emperor's source code from third-party packages.
  • Add code coverage support through Coveralls.
  • Add flake8 to enforce the PEP-8 coding guidelines in every Travis build (#342).
  • Add an all target to get all the needed dependencies for emperor development (pip install emperor[all]).
  • Update FileSaver.js to the latest development version and fixes a bug with large file downloads.
  • Emperor's website can now be found by going to http://emperor.microbio.me

New features

  • Add a slider bar under the Labels tab to select different taxonomies for display.
  • Biplots now include arrows, which represent taxa variances. These can be turned off using the Taxa arrow visibility checkbox.

Emperor 0.9.51 (5 Feb 2015)

  • Improved error message when none of the samples match between coordinates and mapping file.
  • Removed warning due to NumPy 1.9.x.
  • Added support for NumPy 1.9.x.

Emperor 0.9.5 (14 Nov 2014)

  • Add make_emperor.py script auto-generated documentation.
  • Add numpydoc generated documentation setup.
  • Emperor's documentation requires sphinx-boostrap-theme and sphinx.
  • Add documentation about file formats.
  • Updated to three.js revision 68.
  • Fixed problem that removed unique/single-valued categories in the mapping file even if these were selected with --color_by.
  • Added chosen v1.1.0 for drop down menu.
  • Replace MeshLambertMaterial for MeshPhongMaterial to get nicer coloring.
  • Add options to select among different colorbrewer colormaps for continuous coloring.
  • Discrete colors are provided by colorbrewer.
  • The rainbow colormap has disappeared from emperor, see this paper if you want to use that colormap.
  • Remove discrete/continuous coloring checkbox and replace for the color-scheme drop down menu.
  • Add option to select QIIME colors from the color-scheme drop down menu.
  • Emperor now depends on scikit-bio 0.2.1.

Emperor 0.9.4 (10 Sept 2014)

  • Category names are no longer trimmed to 25 characters in the user interface.
  • Change the minimum percent required to display a plot to be greater than 0.01 instead of 0.5.
  • The percent explained by each of the axes is now formatted as a floating point number with two digits in the mantissa.
  • The Key tab now uses all the available space on screen.
  • Improve mouse sensitivity to rotate, pan, zoom-in and zoom out in the 3D plot.
  • Emperor is now hosted under the biocore GitHub organization.
  • Add toggle visible button (Invert Selected) under the Visibility tab, this button will change hidden categories to visible and vice-versa.
  • Supports both NumPy 1.7 and 1.8.
  • Depends on scikit-bio 0.1.4.
  • Emperor provides a Python object that is IPython aware (emperor.Emperor) that will display a usable plot from within the IPython notebook.
  • Each of the categories in the Colors tab displays the # of samples. Also, the labels svg has this information.
  • Emperor will multiply by 100 the percentages explained in the input file if PC1 is lower than 1. This behavior can be stopped using --pct_variation_below_one.

Bug Fixes

  • Fixed problem where coordinate files with large values (greater than 100) would not be displayed on screen.
  • Fixed problem that prevented the user from scrolling through the categories in the user interface.
  • Clean-up the layout of the user interface so it's cleaner and consistent.
  • Fix problem where long category names would alter the layout of the interface.
  • Fix inability to write an 'E' character in the Filename field when exporting an svg.
  • Fix problem where Emperor would generate invalid SVG files for the labels and the plot.
  • Fix inability to reset an animation using the rewind button.
  • Fix one-sample trajectories to not fail during rendering of the animation (these will get ignored).
  • Fix sample identifiers that would fail when the animation started.
  • Fix failure due to passing --missing_custom_axes_values and having a value for all rows in the column of interest. Now is ignored.

New Features

  • Add animations tab to the main user interface.
  • Add unit tests for the JavaScript library code.
  • Support both classic and scikit-bio's coordinate formats.
  • The legends file that emperor generates now has a non-monospace font and a line surrounding each colored square.

Emperor 0.9.3 (5 Dec 2013)

  • Use gradient colors checkbox is now found under the Colors tab.
  • Merge the Options and View tabs; additionally the global opacity slider and global scale slider were moved to their respective tabs.
  • Use gradient colors checkbox now uses the standard blue -> red color gradient
  • Add Emperor to the Python Package Index, now you can install Emperor running pip install emperor.
  • Remove dependency on QIIME and PyCogent.
  • Emperor now depends on qcli and Numpy.

Bug Fixes

  • Add more meaningful error message for biplots when the contingency table passed included only one row.

Emperor 0.9.2 (24 Oct 2013)

Bug Fixes

  • Fixes bug where files named procrustes_results.txt would not be ignored in a plot comparison.

Emperor 0.9.1 (21 Oct 2013)

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 308629f550ff3e108903d3bcf1ce76ce85f4cb96 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.

Emperor 0.9.0 (14 May 2013)

New features:

  • Intuitive and modern graphical user interface.
  • Simple workflow to modify the color of a sample/label from the user interface.
  • Color the labels for the samples by a category in the mapping file.
  • Scale the elements in the plot by the percentage explained from the user interface.
  • Notify the user when values will be removed from the input files.
  • Search for a sample name from the graphical user interface.
  • Show a selector in the plot when double-clicking a sample name.
  • Show and hide samples by a category in the mapping file.
  • Change the opacity of spheres/ellipses from the graphical user interface.
  • Change the size of a sphere from the graphical user interface.
  • Biplots can be created with a custom axis.
  • The color of the biplot spheres can now be changed from the user interface.
  • Extensive script usage testing
  • Addition of contextualized error messages.
  • Reduced output size for datasets with rich mapping files.

Performance improvements:

  • Improved performance and responsiveness from the graphical user interface.
  • Superior graphics quality; elements are rendered in the graphics card not in the CPU.
  • Enhanced performance to create the output files.