# Meta Clustering with Similarity Network Fusion

## Documentation for package ‘metasnf’ version 2.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I J L M N P Q R S T U V W

## -- A --

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
age_df | Mock age data
alluvial_cluster_plot | Alluvial plot of patients across cluster counts and important features
anxiety | Mock ABCD anxiety data
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.settings_df | Coerce a 'settings_df' class object into a 'data.frame' class object
as.data.frame.snf_config | Coerce a 'settings_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.data.frame.t_ext_solutions_df | Coerce a 't_ext_solutions_df' class object into a 'data.frame' class object
as.data.frame.t_solutions_df | Coerce a 't_solutions_df' class object into a 'data.frame' class object
as.data.frame.weights_matrix | Coerce a 'weights_matrix' 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.list.sim_mats_list | Coerce a 'sim_mats_list' class object into a 'list' class object
as.list.snf_config | Coerce a 'snf_config' class object into a 'list' class object
as.matrix.ari_matrix | Coerce a 'ari_matrix' class object into a 'matrix' class object
as.matrix.weights_matrix | Coerce a 'weights_matrix' class object into a 'matrix' class object
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
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
auto_plot | Automatically plot features across clusters

## -- B --

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

## -- C --

cache_a_complete_example_ext_sol_df | Cached example extended solutions data frame
cache_a_complete_example_lp_ext_sol_df | Cached example extended solutions data frame
cache_a_complete_example_sol_df | Cached example solutions data frame
calculate_coclustering | Calculate co-clustering data
calculate_db_indices | Quality metrics
calculate_dunn_indices | Quality metrics
calculate_silhouettes | Quality metrics
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
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 clustering algorithms list
cocluster_density | Density plot of co-clustering stability across subsampled data
cocluster_heatmap | Heatmap of observation co-clustering across resampled data
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

## -- D --

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
dlapply | Apply-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

## -- E --

esm_manhattan_plot | Manhattan plot of feature-cluster association p-values
estimate_nclust_given_graph | Estimate number of clusters for a similarity matrix
euclidean_distance | Built-in distance functions
expression_df | Modification of SNFtool mock data frame "Data1"
extend_solutions | Extend a solutions data frame to include outcome evaluations

## -- F --

fav_colour | Mock ABCD "colour" data

## -- G --

gender_df | Mock gender data
get_complete_uids | Pull complete-data UIDs from a list of data frames
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
gower_distance | Built-in distance functions

## -- H --

hamming_distance | Built-in distance functions

## -- I --

income | Mock ABCD income data
is_data_list | Test if the object is a data list

## -- J --

jitter_plot | Jitter plot separating a feature by cluster

## -- L --

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 non-clustered observations
linear_adjust | Linearly correct data list by features with unwanted signal

## -- M --

mc_manhattan_plot | Manhattan plot of feature-meta cluster association p-values
merge.clust_fns_list | Merge 'clust_fns_list' objects
merge.data_list | Merge observations between two compatible data lists
merge.dist_fns_list | Merge 'dist_fns_list' objects
merge.ext_solutions_df | Merge 'ext_solutions_df' objects
merge.settings_df | Merge 'settings_df' objects
merge.sim_mats_list | Merge 'sim_mats_list' objects
merge.snf_config | Merge method for SNF config objects
merge.solutions_df | Merge 'solutions_df' objects
merge.t_ext_solutions_df | Merge 't_ext_solutions_df' objects
merge.t_solutions_df | Merge 't_solutions_df' objects
merge.weights_matrix | Merge 'weights_matrix' 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"
mock_ari_matrix | Mock example of an 'ari_matrix' metasnf object
mock_clust_fns_list | Mock example of a 'clust_fns_list' metasnf object
mock_data_list | Mock example of a 'data_list' metasnf object
mock_dist_fns_list | Mock example of a 'dist_fns_list' metasnf object
mock_ext_solutions_df | Mock example of a 'ext_solutions_df' metasnf object
mock_mc_solutions_df | Mock example of a 'mc_solutions_df' metasnf object
mock_rep_solutions_df | Mock example of a 'rep_solutions_df' metasnf object
mock_settings_df | Mock example of a 'settings_df' metasnf object
mock_snf_config | Mock example of a 'snf_config' metasnf object
mock_solutions_df | Mock example of a 'solutions_df' metasnf object
mock_t_solutions_df | Mock example of a 't_solutions_df' metasnf object
mock_weights_matrix | Mock example of a 'weights_matrix' metasnf object

## -- N --

new_solutions_df | Constructor for 'solutions_df' class object

## -- P --

plot.ari_matrix | Heatmap of pairwise adjusted rand indices between solutions
plot.data_list | Plot of feature values in a data list
plot.ext_solutions_df | Plot of cluster assignments in an extended solutions data frame
plot.settings_df | Heatmap for visualizing an SNF config
plot.snf_config | Heatmap for visualizing an SNF config
plot.solutions_df | Plot of cluster assignments in a solutions data frame
plot.t_ext_solutions_df | Plot of cluster assignments in an extended solutions data frame
plot.t_solutions_df | Plot of cluster assignments in a solutions data frame
plot.weights_matrix | Heatmap for visualizing an SNF config
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.sim_mats_list | Print method for class 'sim_mats_list'
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

## -- Q --

quality_measures | Quality metrics

## -- R --

rbind.ext_solutions_df | Row-binding of solutions data frame class objects
rbind.solutions_df | Row-binding of solutions data frame class objects
rbind.t_solutions_df | Row-binding of t_solutions_df class objects
rbind.weights_matrix | Row-bind weights matrices
rename_dl | Rename features in a data list
resample | Helper resampling function found in ?sample

## -- S --

save_heatmap | Save a heatmap object to a file
settings_df | Build a settings data frame
sew_euclidean_distance | Built-in distance functions
shiny_annotator | Launch a shiny app to identify meta cluster boundaries
similarity_matrix_heatmap | Plot heatmap of similarity matrix
sim_mats_list | Create or extract a 'sim_mats_list' class object
siw_euclidean_distance | Squared (including weights) Euclidean distance
snf_config | Define configuration for generating a set of SNF-based cluster solutions
sn_euclidean_distance | Built-in distance functions
spectral_eigen | Built-in clustering algorithms
spectral_eigen_classic | Built-in clustering algorithms
spectral_eight | Built-in clustering algorithms
spectral_five | Built-in clustering algorithms
spectral_four | Built-in clustering algorithms
spectral_nine | Built-in clustering algorithms
spectral_rot | Built-in clustering algorithms
spectral_rot_classic | Built-in clustering algorithms
spectral_seven | Built-in clustering algorithms
spectral_six | Built-in clustering algorithms
spectral_ten | Built-in clustering algorithms
spectral_three | Built-in clustering algorithms
spectral_two | Built-in clustering algorithms
split_parser | Helper function to determine which row and columns to split on
str.ari_matrix | Structure of a 'ari_matrix' object
str.clust_fns_list | Structure of a 'clust_fns_list' object
str.data_list | Structure of a 'data_list' object
str.dist_fns_list | Structure of a 'dist_fns_list' object
str.ext_solutions_df | Structure of a 'ext_solutions_df' object
str.settings_df | Structure of a 'settings_df' object
str.sim_mats_list | Structure of a 'sim_mats_list' object
str.snf_config | Structure of a 'snf_config' object
str.solutions_df | Structure of a 'solutions_df' object
str.t_ext_solutions_df | Structure of a 't_ext_solutions_df' object
str.t_solutions_df | Structure of a 't_solutions_df' object
str.weights_matrix | Structure of a 'weights_matrix' object
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
summary.ari_matrix | Summary method for class 'ari_matrix'
summary.clust_fns_list | Summary method for class 'clust_fns_list'
summary.data_list | Summary method for class 'data_list'
summary.dist_fns_list | Summary method for class 'dist_fns_list'
summary.ext_solutions_df | Summary method for class 'ext_solutions_df'
summary.settings_df | Summary method for class 'settings_df'
summary.sim_mats_list | Summary method for class 'sim_mats_list'
summary.snf_config | Summary method for class 'snf_config'
summary.solutions_df | Summary method for class 'solutions_df'
summary.t_ext_solutions_df | Summary method for class 't_ext_solutions_df'
summary.t_solutions_df | Summary method for class 't_solutions_df'
summary.weights_matrix | Summary method for class 'weights_matrix'

## -- T --

train_test_assign | Training and testing split

## -- U --

uids | Pull UIDs from an object

## -- V --

validate_solutions_df | Validator for 'solutions_df' class object
var_manhattan_plot | Manhattan plot of feature-feature association p-values

## -- W --

weights_matrix | Generate a matrix to store feature weights