Changelog • metasnf

metasnf 1.1.2

update settings matrix vignette to avoid convergence error on some seeds

metasnf 1.1.1

CRAN release: 2024-11-08

inclusion column bugfixes from 1.1.0

metasnf 1.1.0

Verbose parameter added to printing functions. By default set to FALSE.
CRAN compliant @return values in documentation.

metasnf 1.0.0

Last update before CRAN submission.

Breaking changes

Changing seed during settings matrix generation has been deprecated. Please manually call set.seed prior to generate_settings_matrix instead.

Other

Package size reduced by downscaling vignette images

metasnf 0.7.2

Bug fix

Function estimate_nclust_given_graph() occasionally yielded incorrect number of cluster estimates as a result of improper scaling in metasnf v0.7.0. The scaling should be corrected now.

Breaking changes

Considerable changes have been made to the co-clustering workflow, including new heatmap and density plot.

metasnf 0.7.1

Possible breaking changes

Occasionally, spectral clustering results may yield an n-cluster solution where n differed from the number of clusters requested as a parameter in the spectral clustering function itself. Now, the spectral clustering functions provided in metasnf have been updated to report the actual number of clusters in the generated solution, rather than the number of clusters that was requested

metasnf 0.7.0

Minor changes

warnings provided when generating a data list with duplicate feature names
warnings provided when using mc_manhattan_plot() with a data list containing duplicate feature names
mc_manhattan_plot() parameter rep_solution replaced with more accurate name extended_solutions_matrix (solutions matrix with _pval columns)

Bug fix

SNFtool::estimateNumberOfClustersGivenGraph() could occasionally error out on the basis of calculating eigenvectors (eigengap heuristic) for a Laplacian with floating point values that were too small. Adapted function estimate_nclust_given_graph() slightly scales up Laplacian to reduce the risk of encountering this error (presumably without any change to resulting cluster number estimate)

metasnf 0.6.8

New functionality

get_matrix_order has arguments allowing users to control which distance metric and agglomerative hierarchical clustering methods are used to sort matrices

metasnf 0.6.7

Minor changes

More consistent usage of “feature” over “variable” across documentation.
New mock ABCD dataframes - like the old ones, but without the “abcd_” prefix and with a more accurate “unique_id” UID column rather than “patient”

metasnf 0.6.6

New functionality

get_complete_uids quickly pulls UIDs of observations with complete data from a list of dataframes

metasnf 0.6.5

Bug fix

extend_solutions doesn’t crash on multi-feature target lists

metasnf 0.6.4

Minor changes

Warning message provided when subjects are dropped during generate_data_list()
New remove_missing parameter for generate_data_list allowing subjects with incomplete data to remain in the data list

metasnf 0.6.3

Bug fixes

ensure cluster variable is treated as factor during autoplotting
bugfix on autoplots built from tibbles rather than dataframes

Improvements

Added clarity to lp_solutions_matrix error message when training set is not subset of full data list
generate_data_list list elements now are named after their components
added heatmap parameters to increase plotting flexibility

New functionality

added generic save_plot function and option to pass cluster_df directly into auto_plot (useful for label propagation)
add merge_data_lists functionality to horizontally merge data lists

metasnf 0.6.2

Bug fixes

extend_solutions() will no longer crash when a data_list has the UID column in non-first position.
generate_data_list() enforces the UID column to be in first position of each dataframe.

metasnf 0.6.1

New functionality

auto_plot() will automatically generate bar and/or jitter plots showing how features in a data_list/target_list are distributed across a single cluster solution

metasnf 0.6.0

New functionality

shiny_annotator() function can be used to identify indices of meta clusters within an adjusted_rand_index_heatmap
adjusted_rand_index_heatmap() now has a split_vector parameter that will slice a heatmap into meta clusters
rename_dl() can be used to rename features in a data_list
manhattan_plot has been split into var_manhattan_plot (key variable - all variables), esm_manhattan_plot (cluster solutions in an extended solutions matrix to all variables), and mc_manhattan_plot (like esm_manhattan_plot, but at the meta-cluster level)
get_representative_solutions extracts max-ARI solutions from an extended solutions matrix based on a split_vector containing meta cluster boundaries
batch_nmi calculates NMI scores (see https://branchlab.github.io/metasnf/articles/nmi_scores.html)
extend_solutions will only calculate p-value summary measures (min/max/mean) for data_list passed in as a target_list parameter, but will also accept and calculate p-values for a data_list passed in through the data_list parameter
heatmap function adjusted_rand_index_heatmap and assoc_pval_heatmap have updated parameters to improve ease of use and flexibility (including easier colour control)

Deprecated functions

get_clustered_subs has been removed (does the same thing as get_cluster_df)
get_cluster_pval deprecated for calc_assoc_pval
All functions related to target_lists specifically have been deprecated in favour of simply using generate_data_list() and its corresponding functions

Name changes

remove_signal has been renamed to linear_adjust to better reflect its function
summarize_distance_metrics_list has been shortened to summarize_dml
correlation_pval_heatmap has been renamed to assoc_pval_heatmap
calc_om_aris has been renamed to calc_aris

New vignettes

NMI scores: https://branchlab.github.io/metasnf/articles/nmi_scores.html
Imputations: https://branchlab.github.io/metasnf/articles/imputations.html

Other changes

Vignettes have been updated
Warnings are raised if spectral clustering does not generate a cluster solution matching the number of clusters requested
Chi-squared and extend_solutions p-value calculation warnings are now suppressed

metasnf 0.5.0

Breaking changes

All variables and values referencing p-values have been rephrased to end in _pval instead of a mix of p_val, pval, and p.
Removal of deprecated functions pval_select, p_val_select, top_oms_per_cluster, check_subj_orders_for_lp, get_p, chi_sq_pval,
Function pval_summaries, which would calculate min/max/mean p-values, has been replaced with summarize_pvals
train_test_assign now provides results as named list of subject vectors instead of a data.frame. keep_split function has been removed accordingly.

Other changes

sort_subjects parameter added to generate_data_list to allow for sorting of subjects in the data_list

metasnf 0.4.6

fix bug in extend_solutions that incorrectly assigns p-values to variable columns through grep (substring instead of exact match)

metasnf 0.4.5

extend_solutions can now also be parallelized (see ?extend_solutions)
remove_signal function has sig_digs parameter that can be used to restrict how many significant figures are returned in the resulting residuals

metasnf 0.4.4

calc_om_aris is now MUCH faster after removing excessive calls to as.numeric and enabling parallel processing with future.apply. Thanks for the idea, Alper.

metasnf 0.4.3

Reformatting of extend_solutions to better handle extreme p-values (e.g. infinity)
Replacement of p_val_select with pval_select which can also return negative-log p-values

metasnf 0.4.2

Bug fixes

generate_data_list correctly errors when components are only partially named (resolves https://github.com/BRANCHlab/metasnf/issues/10)

metasnf 0.4.1

Breaking changes

lp_row function has been replaced by lp_solutions_matrix. The new function is order agnostic: full data lists can be constructed without any restriction on how training and testing set subjects are sorted. Subjects present in the provided solutions matrix to propagate are assumed to be the training subjects.

New functionality

calc_om_aris now has progress parameter. When set to true and used in conjunction with progressr::with_progress(), a progress bar is shown for the calculations. Learn more with ?calc_om_aris.

Bug fixes

grepl instead of grep used in extend_solutions to reduce errors when no chi-squared warning occurs

Other changes

A vignette specifically for label propagation has been added
Full removal of several previously deprecated functions
Minor source code reformatting

metasnf 0.4.0

New functionality

Parallel processing is now available! Check out the vignette here: https://branchlab.github.io/metasnf/articles/parallel_processing.html

metasnf 0.3.3

Breaking changes

input_wt and domain_wt are removed from settings_matrix and rest of package - weighting at this level is no longer planned. This will result in altered settings matrices, but only superficially - the columns “input_wt” and “domain_wt” will be missing, but had no effect on the SNF prior to this patch anyway.

metasnf 0.3.2

keep_split will preserve observations who were assigned a split but were not present in the dataframe being split. Instead of being removed, those observations will have NA values.

metasnf 0.3.1

Bug fixes

fixed fraction_clustered_together crashing when a cluster was assigned to only a single observation
fixed fraction_clustered_together not running due to bracket typo when evaluating length of the data_list

New functionality

correlation_pval_heatmap function can have significance stars disabled with significance_stars parameter

Other changes

pkgdown site now has google site verification code

metasnf 0.3.0

Breaking changes

The original SNFtool function estimateNumberOfClustersGivenGraph has been used up to this point without specifying a parameter for NUMC. Consequently, final similarity matrices clustered with the default methods (spectral clustering based on eigen-gap or rotation cost heuristics) were not capable of resulting in more than 5 clusters. The default functions have been updated to span 2 clusters to 10 clusters. Users will likely see different clustering results as a result of this change. To replicate the behaviour of default spectral clustering prior to v0.3.0, users should copy the following code prior to the batch_snf command:

clust_algs_list <- generate_clust_algs_list(
    "spectral_eigen" = spectral_eigen_classic,
    "spectral_rot" = spectral_rot_classic
)

# Adapt below as necessary
solutions_matrix <- batch_snf(
    data_list,
    settings_matrix,
    clust_algs_list = clust_algs_list
)

Added “workspace=2e7” parameter to fisher_exact_pval function to avoid “FEXACT” error (like here https://github.com/Lagkouvardos/Rhea/issues/17). Impact on results is expected to be negligible.

New functionality

Function remove_signal() enables correcting a data_list linearly for confounders / unwanted signal. Vignette is available: https://branchlab.github.io/metasnf/articles/confounders.html.
batch_snf() has new parameter automatic_standard_normalize to switch out the default numeric distance measures (euclidean) with standard normalized variants.

Other changes

Added a NEWS.md file to track changes to the package.