Meta Clustering with Similarity Network Fusion

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Documentation for package ‘metasnf’ version 2.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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