Migrating from CytoRSuite to CytoExploreR

[DillonHammill]

CytoExploreR is finally here!

CytoRSuite has completely been re-designed to be more intuitive and provide a framework for developing user friendly tools for cytometry data analysis. Thanks you to everyone who provided feedback on CytoRSuite, I hope that you find the features you requested in CytoExploreR.

Please read the new documentation carefully! CytoExploreR will have some familiar features, but should be treated as a completely new package so that you don't miss subtle changes. Countless improvements have been made to improve the user friendliness, robustness, speed and plenitude of the package. Some of the key improvements are summarised below:

cyto_plot

• number of events to plot can now be specified through the display argument, this arguments has been set to 25 000 events by default. CytoExploreR will make sure that overlays are appropriately sampled to retain original ratios.
• new axes_limits argument makes it easy to adjust the axes limits without having to specify them manually. Try setting this argument to "machine", "data" and "auto" to see how it affects the axes limits.
• the default smoothing parameter density_smooth has been set to 0.6 to better display the data as it appears in 2D plots.
• each data layer in 1D plots now uses the same binwidth for each density distribution.
• contour_lines can now be added to each data layer and are no longer cut off.
• axes text can now be removed through the axes_text argument.
• legends are now positioned in the center of the plot.
• users now have control over the gate fill colour through the gate_fill argument.
• labels are now automatically positioned to minimize overlap.
• labels can now be interactively positioned through mouse click by setting label_position to manual.
• plot background and border colours can now be changed through the the border_line and border_fill arguments. Black plots here we come!
• statistics for events outside of gates can also be displayed by setting the negate argument to TRUE.
• cyto_plot now handles empty data layers.
• density distributions can now be stacked without setting density_modal to TRUE.
• users can supply manual colour palettes for points and density distributions through the point_cols and density_cols arguments.
• the density colour scale used in 2D plots can now be manually supplied by the user through the point_col_scale argument.
• axes labels, plot titles and legends now contain more relevant text.
• custom themes are now supported through cyto_plot_theme.

cyto_plot_explore

• new plotting function to visualise data in all possible parameter combinations in 2D scatter plots.

cyto_plot_gating_tree

• new interactive visualisation tool to explore the gating tree structure.

cyto_plot_compensation

• improved support for plotting compensated and transformed samples.

cyto_plot_save

• new function to save high resolution cyto_plot images for publication.

cyto_gate_draw

• negated gates are now supported by setting the negate argument to TRUE, boolean entries are automatically included in the gatingTemplate.
• individually gate samples or groups of samples using the improved group_by argument.
• quadGates have been updated to display correct statistics that account for events shared on the gate crosshair.
• overlays are now appropriately sampled to better display the data.
• CytoRSuite gating functions have been internalised and manually gating goes through cyto_gate_draw now.

cyto_gate_edit

• new grouping can now be supplied to cyto_gate_edit to split samples into groups prior to editing gates.

cyto_gate_rename

• easily rename gates in the GatingSet and gatingTemplate using cyto_gate_rename

cyto_spillover_compute

• added support for single stain controls with internal reference populations rather than universal unstained control.
• populations can now be specified on a per sample basis to obtain more accurate spillover values.
• if multiple controls are supplied for a particular channel, the one with the greatest signal will be used for spillover computation.

cyto_spillover_edit

• added support for supplying fully stained samples.
• improved user experience by automatically selecting channels based on user input.
• median tracker has been updated to be less sensitive to outliers.
• plots tab has been re-vamped with a better colour scheme.

cyto_spillover_spread_compute

• new function to compute spillover spreading matrices using compensation controls.

cyto_stats_compute

• removed automatic saving to prevent overwriting files.
• data can now be returned in either long or wide format.
• return tidyverse friendly output to make it easy to visualise the results using ggplot2.

cyto_map

• new function to produce dimensionality reduced maps of cytometry data (native support for PCA, tSNE, UMAP and EmbedSOM)

cyto_transformers

• CytoExploreR inherits support for data transformations from the flowWorkspace package (including log, arcsinh, biexponential and logicle transformations).
• custom transformations are also supported through the transformerList class.

cyto_gatingTemplate helpers

• new functions to interact directly with the gatingTemplate, set an active gatingTemplate, create a gatingTemplate or apply a gtaingTemplate to a GatingSet.

cyto-helpers

• numerous helper functions have been created to load, annotate, barcode, convert, sort, select, merge, split, sample, transform, compensate, copy or save cytometry data objects.

That's just the beginning, there is so much more to see and do! For more detailed workflows refer to the new CytoExploreR website:
https://dillonhammill.github.io/CytoExploreR/

I will also be posting specific features as issues on this page until all the features are documented on the website.

I will be ending support for CytoRSuite at the end of the month, all future updates will be made to CytoExploreR. Thanks again to everyone who provided feedback on CytoRSuite, without your support I would not have been able to develop CytoExploreR!

Have fun exploring your cytometry data with CytoExploreR!