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Changelog

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

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

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

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

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
)

New functionality

Other changes

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