Meta Clustering with Similarity Network Fusion


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Documentation for package ‘metasnf’ version 2.0.0

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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
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
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 --

calculate_coclustering Calculate coclustering 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 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

-- 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 Lapply-like function for data list objects
dl_variable_summary Variable-level summary of a data list

-- 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
features Return character vector of features stored in an object

-- G --

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_clusters Extract cluster membership vector from one solutions data frame row
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_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
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 unclustered observations
linear_adjust Linearly correct data list by features with unwanted signal

-- M --

mc_manhattan_plot Manhattan plot of feature-meta cluster associaiton p-values
merge.snf_config Merge method for SNF config objects
merge_df_list Merge list of data frames into a single data frame
merge_dls Horizontally merge compatible data lists
meta_cluster_heatmap Heatmap of pairwise adjusted rand indices between solutions
methylation_df Modification of SNFtool mock data frame "Data2"

-- N --

new_solutions_df Constructor for 'solutions_df' class object
n_features Extract number of features stored in an object
n_observations Extract number of observations stored in an object

-- P --

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 'weights_matrix'
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 --

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

-- 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
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

-- 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