NEWS.md
In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

CytoExploreR 1.1.0

Fix cyto_gate_bool() to anchor new nodes to most recent ancestor in the GatingSet.
Fix labelling of transformed axes within cyto_plot().
Fix statistics computation in cyto_plot() when gates and overlays are present.
Fix cyto_plot_gating_scheme() to allow the use of custom colour scale when back_gate = TRUE.
Make sure cyto_load() is able to read in saved GatingSets.

CytoExploreR 1.0.8

Add select argument to cyto_stats_compute() to allow computation of statistics for a subset of samples based on experimental variables.
Add new cyto_gate_bool() function to add boolean gates to the GatingSet and gatingTemplate.
Improve cyto_channels_restrict() to drop unused channels in cytometry objects. Add an exclude argument to forcibly remove FSC, SSC or Time parameters. The restrict argument in cyto_setup() now accepts a vector of channels to be passed internally to the exclude argument of cyto_channels_restrict().
Add support for forward gating by colouring points based on the expression of a particular marker in cyto_plot(), simply pass the name of the marker to the point_col argument.
Update default density colour scale for points to include a darker blue at the lower end of the scale. This provides better resolution at the lower end of the scale and balances the colour gradient.
Add channels argument to cyto_extract() to restrict data to certain channels when it is extracted from a GatingHierarchy or GatingSet.
Add new function cyto_names_parse() to split file names into experiment variables in cyto_details(). Files should be named with each variable separated by a delimiter. For example, file named 160520-Exp1-StimA.fcs can be separated into variables date, experiment and treatment. parse_names argument has been added to cyto_setup() to allow name parsing when files are loaded in.
Custom functions can now be supplied by name to the type argument in cyto_map(). This means that you can use any available dimensionality reduction technique or create your own one to map your data.
Add cyto_gatingTemplate_generate() to obtain a CytoExploreR-ready gatingTemplate from any GatingHierarchy or GatingSet.
Improve speed of plotting using cyto_plot() by increasing computation speed of axes ranges.
Add support for scattermore to further improve cyto_plot() plotting speed. To use this feature, users will need to manually install scattermore and set options("cyto_plot_fast" = TRUE). Setting options("cyto_plot_fast" = FALSE) will return to using conventional plotting. It is recommended to use conventional plotting when saving images with cyto_plot_save() to obtain high resolution images.
Fix quadrant gate bug in cyto_gate_edit() to allow editing of quadrant gates.
Fix computation of statistics for stacked density distributions in cyto_plot().
Fix cyto_marker_edit() to accept custom file name for saving and add support for marker removal.
Hide messages when opening data editors and only open data editors in interactive mode.
Improve visualization of quadrant gates to distinguish them from traditional rectangleGates. Quadrant gates can now be individually visualized (i.e. users can indicate which quadrants to display).
Added new function cyto_nodes_convert() to anchor ambiguous nodes to a known parental node within cyto_plot().

CytoExploreR 1.0.7

Fix quadrant gating bug in cyto_gate_draw().
cyto_map() can now appropriately handle empty flowFrames/cytoframes.
Switch to using rsvd::rpca() for faster PCA computation in cyto_map().
Add versioned and latest tags to CytoExploreR Docker images for reproducibility. Docker images are always built against the most recent RGLab packages at the time. Versioned Docker images allow users to go back in time should they need to.
Update FIt-SNE to version 1.2.1. This change requires updated installation of FIt-SNE and now requires the rsvd package. FIt-SNE now uses PCA initialization by default.
Configure Docker images with FIt-SNE and search for fast_tsne location automatically. Hide this directory to prevent accidental deletion.
Add FIt-SNE configuration instructions on GitHub Issue #29. Configuration instructions for mac OS are still a work in progress.
Make improvements to flowAI package to improve compatibility with CytoExploreR. FlowAI can be used when loading samples in cyto_setup() by setting clean = TRUE or manually applied downstream using cyto_clean().
Add back Appveyor CI to build on windows.

CytoExploreR 1.0.6

Update custom plotting functions (cyto_plot_save, cyto_plot_layout, cyto_plot_custom and cyto_plot_complete) to allow complex layouts. Layouts must now be supplied to these functions either as a vector or matrix.
cyto_plot_complete no longer closes the RStudio or X11 graphics devices.
Add new margins argument to cyto_plot to allow customization of plot margins.
Fix overlay = "children" when plotting GatingSet objects with cyto_plot.

CytoExploreR 1.0.5

Add ability to control plotting order in cyto_plot when using the group_by argument.
Add new data_editor function to bring excel-like features to all context menus and data editors.
Add viewer argument to cyto_spillover_edit to allow it to be launched in the RStudio viewer pane (if desired).

CytoExploreR 1.0.4

Remove requirement for GUI device in cyto_gate_draw and cyto_gate_edit. Users can now draw gates directly on the RStudio graphics device.
Add support for changing gate point and lines colours within cyto_gate_draw and cyto_gate_edit.
improve appearance of 1-D interval gates in cyto_gate_draw.
Add dependency for openCyto >= 1.25.2 to support gating of empty populations.
Add Dockerfile and Makefile to build CytoExploreR docker images for reproducible data analysis. Docker images can be pulled from docker hub at dhammill/cytoexplorer.

CytoExploreR 1.0.3

Update installation instructions on website following in changes in RGLab default branches.
Fix sample grouping when no experiment details are added to samples.
Resort to machine axes limits when no events are present for plotting.
Improve handling of multiple compensation controls for the same channel in cyto_spillover_compute(). Now the control with the best signal will be used for the calculation.
Add support to cyto_map() for FIt-SNE dimensionality reduction. Update cyto_map() documentation to include references for each of the supported dimensionality reduction algorithms.
Fix gating of empty populations to prevent dummy gates being returned by openCyto.
Frequency statistics for empty populations are now displayed as zero instead of NaN.
Improve handling of arguments within cyto_plot for better user experience.
Fix errors for cyto_spillover_compute and cyto_spillover_spread_compute on mac OS.
cyto_setup() now accepts filenames through markers and details arguments.