greatR 2.0.0

Added {patchwork} as a dependency.
Updated {greatR} logo.
Updated default optimisation_method in register() to be "lbfgsb" (LBFSG-B) instead of "nm" (Nelder-Mead).
Added sample SOC1 arabidopsis_SOC1_data.csv and brapa_SOC1_data.csv extdata.
Refactored optimise_registration_parameters argument in register() to use_optimisation.
Updated register() to return object of S3 class res_greatR.
Updated calculate_distance() to return object of S3 class dist_greatR.
Refactored summarise_registration() as summary.res_greatR() S3 method.

Improvements

Deprecate use of time_delta variable in registration process.
Added fun_args (a list of arguments used when calling the function) in register() results.
Updated summary.res_greatR() to return NA instead of [NA, NA] when all genes are non-registered.
Added reg_params (table containing distribution of registration parameters) to results list in summary.res_greatR() method.
Simplified calc_overlapping_percent() calculation.
Take into consideration overlapping_percent when applying manual registration.
Updated logic of calc_variance() for data with no replicates to consider expression_value.
Updated get_stretch_search_space_limits() and get_shift_search_space_limits() to exclude unexplorable regions in search space.
Improved calculate_distance() and aux get_timepoint_comb_*_data() functions to eliminate column selection and renaming inside lapply() calls, reducing execution time by up to 25%.
Added type ("registered" or "all") and genes_list arguments to calculate_distance() to filter genes.
Added new unit tests.
Updated unit tests, and added S3 class checks where apropriate.
Updated vignettes and README diagrams and figures.
Updated vignettes with additional examples, comments on arguments, and full coverage of all plot() methods.

Fixed get_shift_search_space_limits() to adjust shift space limits accordingly to removal of time_delta variable (see 48c943c).
Fixed default overlapping_percent = 0.5 (instead of 50) in register_manually().
Fixed get_stretch_search_space_limits() to correctly determine lower and upper limits when single stretch value is provided.
Fixed issue in get_shift_search_space_limits() where range variables were not available when calc_mode == "bound".

bind_results() auxiliary function to merge results from register().
theme_greatR() function and greatR_palettes list.
transform_input() S3 generic to accept different types of input in register().
plot.res_greatR() S3 method to replace plot_registration_results().
plot.dist_greatR() S3 method to replace plot_heatmap().
plot.summary.res_greatR() S3 method inspired by WVPlots::ScatterHistC().