abcd_anxiety            Mock ABCD anxiety data
abcd_colour             Mock ABCD "colour" data
abcd_cort_sa            Mock ABCD cortical surface area data
abcd_cort_t             Mock ABCD cortical thickness data
abcd_depress            Mock ABCD depression data
abcd_h_income           Mock ABCD income data
abcd_income             Mock ABCD income data
abcd_pubertal           Mock ABCD pubertal status data
abcd_subc_v             Mock ABCD subcortical volumes data
add_settings_df_rows    Add rows to a settings_df
adjusted_rand_index_heatmap
                        Heatmap of pairwise adjusted rand indices
                        between solutions
age_df                  Mock age data
alluvial_cluster_plot   Alluvial plot of patients across cluster counts
                        and important features
anxiety                 Mock ABCD anxiety data
arrange                 Arrange rows in an object
as.data.frame.data_list
                        Coerce a 'data_list' class object into a
                        'data.frame' class object
as.data.frame.ext_solutions_df
                        Coerce a 'ext_solutions_df' class object into a
                        'data.frame' class object
as.data.frame.solutions_df
                        Coerce a 'solutions_df' class object into a
                        'data.frame' class object
as.list.clust_fns_list
                        Coerce a 'clust_fns_list' class object into a
                        'list' class object
as.list.data_list       Coerce a 'data_list' class object into a 'list'
                        class object
as.list.dist_fns_list   Coerce a 'dist_fns_list' class object into a
                        'list' class object
as.matrix.weights_matrix
                        Coerce a 'weights_matrix' class object into a
                        'matrix' class object
as_ari_matrix           Convert an object to an ARI matrix
as_data_list            Convert an object to a data list
as_settings_df          Convert an object to a settings data frame
as_sim_mats_list        Convert an object to a similarity matrix list
as_snf_config           Convert an object to a snf config
as_weights_matrix       Convert an object to a weights matrix
assemble_data           Collapse a data frame and/or a data list into a
                        single data frame
assoc_pval_heatmap      Heatmap of pairwise associations between
                        features
auto_plot               Automatically plot features across clusters
bar_plot                Bar plot separating a feature by cluster
batch_snf               Run variations of SNF.
batch_snf_subsamples    Run SNF clustering pipeline on a list of
                        subsampled data lists.
calc_aris               Construct an ARI matrix storing inter-solution
                        similarities
calc_assoc_pval_matrix
                        Calculate p-values for all pairwise
                        associations of features in a data list
calc_nmis               Calculate feature NMIs for a data list and a
                        solutions data frame
calculate_coclustering
                        Calculate coclustering data.
cancer_diagnosis_df     Mock diagnosis data
cell_significance_fn    Place significance stars on ComplexHeatmap
                        cells.
check_dataless_annotations
                        Helper function to stop annotation building
                        when no data was provided
check_hm_dependencies   Check for ComplexHeatmap and circlize
                        dependencies
check_similarity_matrices
                        Check validity of similarity matrices
clust_fns               Built-in clustering algorithms
clust_fns_list          Build a clusteing algorithms list
cocluster_density       Density plot coclustering stability across
                        subsampled data.
cocluster_heatmap       Heatmap of observation co-clustering across
                        resampled data.
collapse_dl             Convert a data list into a data frame
colour_scale            Return a colour ramp for a given vector
config_heatmap          Heatmap for visualizing an SNF config
cort_sa                 Mock ABCD cortical surface area data
cort_t                  Mock ABCD cortical thickness data
data_list               Build a 'data_list' class object
depress                 Mock ABCD depression data
diagnosis_df            Mock diagnosis data
dist_fns                Built-in distance functions
dist_fns_list           Build a distance metrics list
dl_variable_summary     Variable-level summary of a data list
dlapply                 Lapply-like function for data list objects
dplyr_row_slice.ext_solutions_df
                        Function to extend dplyr to extended solutions
                        data frame objects
dplyr_row_slice.solutions_df
                        Function to extend dplyr to solutions data
                        frame objects
esm_manhattan_plot      Manhattan plot of feature-cluster association
                        p-values
estimate_nclust_given_graph
                        Estimate number of clusters for a similarity
                        matrix
expression_df           Modification of SNFtool mock data frame "Data1"
extend_solutions        Extend a solutions data frame to include
                        outcome evaluations
fav_colour              Mock ABCD "colour" data
features                Return character vector of features stored in
                        an object
gender_df               Mock gender data
generate_clust_algs_list
                        Generate a clustering algorithms list
generate_distance_metrics_list
                        Generate a list of distance metrics
generate_settings_matrix
                        Build a settings data frame
get_cluster_df          Extract cluster membership information from one
                        solutions data frame row
get_cluster_solutions   Extract cluster membership information from a
                        sol_df
get_clusters            Extract cluster membership vector from one
                        solutions data frame row
get_complete_uids       Pull complete-data UIDs from a list of data
                        frames
get_dl_uids             Extract UIDs from a data list
get_heatmap_order       Return the row or column ordering present in a
                        heatmap
get_matrix_order        Return the hierarchical clustering order of a
                        matrix
get_pvals               Get p-values from an extended solutions data
                        frame
get_representative_solutions
                        Extract representative solutions from a matrix
                        of ARIs
income                  Mock ABCD income data
is_data_list            Test if the object is a data list
jitter_plot             Jitter plot separating a feature by cluster
label_meta_clusters     Assign meta cluster labels to rows of a
                        solutions data frame or extended solutions data
                        frame
label_propagate         Label propagate cluster solutions to
                        unclustered observations
linear_adjust           Linearly correct data list by features with
                        unwanted signal
mc_manhattan_plot       Manhattan plot of feature-meta cluster
                        associaiton p-values
merge.data_list         Merge observations between two compatible data
                        lists
merge.snf_config        Merge method for SNF config objects
merge_df_list           Merge list of data frames into a single data
                        frame
meta_cluster_heatmap    Heatmap of pairwise adjusted rand indices
                        between solutions
methylation_df          Modification of SNFtool mock data frame "Data2"
n_features              Extract number of features stored in an object
n_observations          Extract number of observations stored in an
                        object
new_solutions_df        Constructor for 'solutions_df' class object
print.ari_matrix        Print method for class 'ari_matrix'
print.clust_fns_list    Print method for class 'clust_fns_list'
print.data_list         Print method for class 'data_list'
print.dist_fns_list     Print method for class 'dist_fns_list'
print.ext_solutions_df
                        Print method for class 'ext_solutions_df'
print.settings_df       Print method for class 'settings_df'
print.snf_config        Print method for class 'snf_config'
print.solutions_df      Print method for class 'solutions_df'
print.t_ext_solutions_df
                        Print method for class 't_ext_solutions_df'
print.t_solutions_df    Print method for class 't_solutions_df'
print.weights_matrix    Print method for class 'weights_matrix'
pubertal                Mock ABCD pubertal status data
pval_heatmap            Heatmap of p-values
quality_measures        Quality metrics
random_removal          Generate random removal sequence
rbind.ext_solutions_df
                        Row-binding of solutions data frame class
                        objects.
rbind.solutions_df      Row-binding of solutions data frame class
                        objects.
rename_dl               Rename features in a data list
resample                Helper resample function found in ?sample
save_heatmap            Save a heatmap object to a file
settings_df             Build a settings data frame
shiny_annotator         Launch a shiny app to identify meta cluster
                        boundaries
sim_mats_list           Create or extract a 'sim_mats_list' class
                        object
similarity_matrix_heatmap
                        Plot heatmap of similarity matrix
siw_euclidean_distance
                        Squared (including weights) Euclidean distance
snf_config              Define configuration for generating a set of
                        SNF-based cluster solutions
split_parser            Helper function to determine which row and
                        columns to split on
subc_v                  Mock ABCD subcortical volumes data
subsample_dl            Create subsamples of a data list
subsample_pairwise_aris
                        Calculate pairwise adjusted Rand indices across
                        subsamples of data
summarize_clust_fns_list
                        Summarize a clust_fns_list object
summarize_dfl           Summarize metrics contained in a dist_fns_list
summarize_dl            Summarize a data list
summary.data_list       Summary method for class 'data_list'
summary_features        Pull features used to calculate summary
                        p-values from an object
train_test_assign       Training and testing split
uids                    Pull UIDs from an object
validate_solutions_df   Validator for 'solutions_df' class object
var_manhattan_plot      Manhattan plot of feature-feature association
                        p-values
weights_matrix          Generate a matrix to store feature weights
