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All functions

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
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
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
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 co-clustering 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
spectral_eigen() spectral_rot() spectral_eigen_classic() spectral_rot_classic() spectral_two() spectral_three() spectral_four() spectral_five() spectral_six() spectral_seven() spectral_eight() spectral_nine() spectral_ten()
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
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
euclidean_distance() gower_distance() sn_euclidean_distance() sew_euclidean_distance() hamming_distance()
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
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
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
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 non-clustered observations
linear_adjust()
Linearly correct data list by features with unwanted signal
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
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
new_solutions_df()
Constructor for solutions_df class object
plot(<ari_matrix>) meta_cluster_heatmap()
Heatmap of pairwise adjusted rand indices between solutions
plot(<data_list>)
Plot of feature values in a data list
plot(<ext_solutions_df>) plot(<t_ext_solutions_df>)
Plot of cluster assignments in an extended solutions data frame
plot(<snf_config>) config_heatmap() plot(<settings_df>) plot(<weights_matrix>)
Heatmap for visualizing an SNF config
plot(<solutions_df>) plot(<t_solutions_df>)
Plot of cluster assignments in a solutions data frame
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
calculate_silhouettes() calculate_dunn_indices() calculate_db_indices()
Quality metrics
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
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
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
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