NEWS.md
cyto_gate_bool() to anchor new nodes to most recent ancestor in the GatingSet.cyto_plot().cyto_plot() when gates and overlays are present.cyto_plot_gating_scheme() to allow the use of custom colour scale when back_gate = TRUE.cyto_load() is able to read in saved GatingSets.select argument to cyto_stats_compute() to allow computation of statistics for a subset of samples based on experimental variables.cyto_gate_bool() function to add boolean gates to the GatingSet and gatingTemplate.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().cyto_plot(), simply pass the name of the marker to the point_col argument.cyto_extract() to restrict data to certain channels when it is extracted from a GatingHierarchy or GatingSet.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.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.cyto_gatingTemplate_generate() to obtain a CytoExploreR-ready gatingTemplate from any GatingHierarchy or GatingSet.cyto_plot() by increasing computation speed of axes ranges.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.cyto_gate_edit() to allow editing of quadrant gates.cyto_plot().cyto_marker_edit() to accept custom file name for saving and add support for marker removal.cyto_nodes_convert() to anchor ambiguous nodes to a known parental node within cyto_plot().cyto_gate_draw().cyto_map() can now appropriately handle empty flowFrames/cytoframes.rsvd::rpca() for faster PCA computation in cyto_map().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.fast_tsne location automatically. Hide this directory to prevent accidental deletion.cyto_setup() by setting clean = TRUE or manually applied downstream using cyto_clean().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.margins argument to cyto_plot to allow customization of plot margins.overlay = "children" when plotting GatingSet objects with cyto_plot.cyto_plot when using the group_by argument.data_editor function to bring excel-like features to all context menus and data editors.cyto_spillover_edit to allow it to be launched in the RStudio viewer pane (if desired).cyto_gate_draw and cyto_gate_edit. Users can now draw gates directly on the RStudio graphics device.cyto_gate_draw and cyto_gate_edit.cyto_gate_draw.dhammill/cytoexplorer.cyto_spillover_compute(). Now the control with the best signal will be used for the calculation.cyto_map() for FIt-SNE dimensionality reduction. Update cyto_map() documentation to include references for each of the supported dimensionality reduction algorithms.cyto_setup() now accepts filenames through markers and details arguments.