Package index
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add_coherence_metrics() - add_coherence_metrics
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analyze_channel() - analyze_channel
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analyze_file() - analyze_file
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analyze_interval() - analyze_interval
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analyze_project() - analyze_project
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assign_cluster_colors() - Assign colors to clusters
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build_plot_path() - Build the file path for a single plot output
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check_fit() - Plot observed vs fitted time series for a single cell
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check_phase() - Plot phase distribution across cells
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circStats_plot() - Circular stats plot with per-group mean arrows
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circular_plot() - Circular phase plot with optional mean-phase alignment
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clockcyter_example_path() - Path to the toy dataset folder
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computePeriod() - Run FFT-NLLS period analysis on a fluorescence trace matrix
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create_plot() - Dispatch a plot by type
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doughnut_plot() - Doughnut chart of cluster abundance
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extract_vars() - Extract variables from analysis results across files and save as wide tables
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filter_edges() - Filter network edges or vertices belonging to NULL clusters
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generate_plot_type_reports() - generate_plot_type_reports
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generate_plots() - generate_plots
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generate_reports() - generate_reports
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get_grid_coords() - Import and scale grid centroid coordinates
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hist_plot() - Histogram or bar chart of a node variable
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importGridVals() - Import all values from kernel extraction
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importROI() - function to import a single ROI
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index_files() - index_files
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make_params() - make_params
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metric_mean_plot() - Mean ± SE plot of a metric stratified by group with optional significance brackets
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network_analysis() - Build and cluster a cell correlation network
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order_clusters() - Reorder and relabel network clusters
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period_print() - Jitter plot of per-cell period lengths
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phase_distribution() - Kernel density plot of phase distribution for one or two channels
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plot_group_traces() - Mean ± SE trace plot for each group
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plot_overlap_heatmap() - Cluster segregation heatmap
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plot_type_to_name() - Translate a plot-type key to its output filename stem
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prepare_file() - prepare_file
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preprocess_data() - Remove outliers, smooth, and detrend fluorescence traces
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pull_plots() - Copy plot files into a centralised output directory
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pull_rds() - Copy RDS result files into a centralised output directory
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ranges_calculation() - Compute per-variable display ranges across all files and intervals
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setup_example() - Copy the toy dataset to a writable location
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spatial_clusters_plot() - Spatial scatter plot of cluster assignments
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threeDplot() - Interactive 3D scatter plot via plotly
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traces_correlation() - collection of funtions used in network analysis Compute pairwise cell correlations and return edge list
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validate_params() - validate_params