- fixed a bug in
visualize_KEGG_diagram()whereggkeggwas raising an error (#214)
- fixed a bug regarding KEGG gene set fetching: removed the conversion functionality in
get_kegg_gsets()which now returns KEGG IDs so that the user can convert the returned identifiers using a more appropriate tool (e.g. BioMart) should they wish
- implemented a new
color_kegg_pathway()function usingggkeggto create colored KEGG pathway ggplot objects (instead of usingKEGGRESTto obtain the colored PNG files, which no longer works #169) - renamed the
visualize_hsa_KEGGfunction tovisualize_KEGG_diagram()to reflect this is now able to handle KEGG pathway enrichment results from any organism - updated the
visualize_terms(),visualize_term_interactions()andvisualize_KEGG_diagram()functions so that they now return a list of ggplot objects (named by term ID) - updated the
get_kegg_gsets()function to also useggkeggfor fetching genes per pathway data - removed unneeded dependencies:
magick,KEGGgraphandKEGGREST
- updated the
get_biogrid_pin()function so that it can now determine the latest version and download/process it from BioGRID (via settingrelease = "latest", which is now the default behavior)
- fixed a bug in the
UpSet_plot()plot function regarding the interaction withggupsetpackage that was discovered in a reverse dependency check forggplot2 3.5.0(#189) - fixed gene symbol case mismatch issue in
score_terms()(#186) - applied enhancement suggestion from #184 to enable scale fill manual for
term_gene_graph()
- reverted removal of
create_HTML_report()sorun_pathfindR()once again generates HTML reports
- added the
disable_parallelargument inactive_snw_enrichment_wrapper()to be able to disable parallel runs viaforeach - fixed the issue encountered on CentOS where
forechwasn't loadingpathfindR(#164) - fixed a CRAN error due to a package documentation issue (#172)
- performed some refactoring and updated/improved all tests
- removed
create_HTML_report()sorun_pathfindR()no longer generates a HTML report
- added the
dir_for_reportargument in the internal functioncreate_HTML_report()to fix test issues on CRAN
- updated the java active subnetwork search component and added the
seedForRandomargument inactive_snw_search()to ensure reproducibility. By default behavior, inrun_pathfindR(), a seed is set for each iteration to produce reproducible results (#108) - as the example input/output data were renamed for convenience in 'pathfindR.data' v2.0, 'pathfindR' now depends on pathfindR.data (>= 2.0)
- refactored/simplified
run_pathfindR() - visualization enriched term diagrams are now NOT part of
run_pathfindR() - default behavior of
run_pathfindR()is now to run in a temporary directory. The user can still setoutput_dirto run in a specified directory and also produce HTML reports - in
hierarchical_term_clustering(), update the sequence of number of clusters for which silhouette width is calculated for choosing the optimal number of clusters. This should speed up the function for cases with a large number of enriched terms - updated the relevant vignettes to reflect the implemented changes
- fixed a minor issue in
return_pin_path()where the PIN was not properly read (#157)
- updated the alias selection function within
input_processing()so that an alias that is not already present is selected - updated the min-max scaling (controlled by
scale_vals) incolor_kegg_pathway(), the default is nowscale_vals=TRUE - updated the
term_gene_heatmap()function so that legend title is shown and can be customized - updated the
term_gene_heatmap()function so that coloring is proper when no change values are provided ingenes_df - added the
sort_terms_by_pargument to theterm_gene_heatmap()function to enable sorting of terms by 'lowest_p' - in visualization functions, made coloring of up-/down-regulated genes consistent (#126)
- added the
vertex.label.cexandvertex.size.scalingarguments tocluster_graph_vis() - added the
show_legendargument tovisualize_term_interactions()to toggle the legend
- Fixed coloring issue in
color_kegg_pathway() - In
color_kegg_pathway()the default value fornormalize_valsis nowFALSE
- fixed an issue in
get_kegg_gsets()where empty result was returned for some organisms due to an error in parsing (#72)
- added
repel = TRUEinterm_gene_graph()andcombined_results_graph()for better visualization of labels - fixed minor issue in
enrichment_chart()(#75) - fixed minor issue in
visualize_term_interactions() - fixed issue in
get_biogrid_pin()where the download method was set towget(now set toauto, per #83) - updated to using tab3 format for
get_biogrid_pin()(if tab3 is available for the chosen release, otherwise tab2 format is used) - updated the default version of PIN obtained by
get_biogrid_pin()to '4.4.200' - in
get_kegg_gsets(), improved parsing of KEGG term descriptions so that no description is duplicated (#87) - in
score_terms(), if using descriptions, the ID is now appended for (any) duplicated term descriptions (#87) - in
obtain_colored_url(), swappedbg_colorwithfg_colordue to an issue withKEGGREST - added legend to
term_gene_heatmap()(#95) - in
get_biogrid_pin(), the "download.file.method" from global options is used combined_results_graph()raises an error if there are no common terms in the combined data frame
- In
run_pathfindR(), the defaultiterationswas set back to 10 (the default for all other v1.x)
- In
run_pathfindR(), as "GR" (the default active subnetwork search method) provides nearly identical results in each iteration, the defaultiterationsis set to 1 - added the column 'support' (the proportion of active subnetworks leading to enrichment over all subnetworks) in the output
- updated the download URL in
get_biogrid_pin()as BioGRID updated the URL for download
- changed old argument in the "Step-by-Step Execution of the pathfindR Enrichment Workflow" vignette
- fixed an issue in
visualize_term_interactions()where the file name was too long, it was causing an error on Windows. Limited to 100 characters (#58)
- Fixed issue in
check_java_version()where java version 14 could not be parsed (#49) - Fixed issue in
combined_results_graph()where gene nodes were not colored correctly (#55)
- created separate package
pathfindR.datafor storing pathfindR data - added the function
visualize_active_subnetworks()for visualizing graphs of active subnetworks - add the new vignette "Comparing Two pathfindR Results" that briefly describes how different pathfindR results can be compared
- added the functions
combine_pathfindR_results()andcombined_results_graph()for comparison of 2 pathfindR results and term-gene graph of the combined results, respectively - added the function
get_pin_file()for obtaining organism-specific PIN data (only from BioGRID for now) - added the function
get_gene_sets_list()for obtaining organism-specific gene sets list from KEGG, Reactome and MSigDB - added the function
term_gene_heatmap()to create heatmap visualizations of enriched terms and the involved input genes. Rows are enriched terms and columns are involved input genes. Ifgenes_dfis provided, colors of the tiles indicate the change values - added the function
UpSet_plot()to create UpSet plots of enriched terms - added the human cell markers gene sets data
cell_markers_gsetsandcell_markers_descriptions
- fixed an issue regarding
parallel::makeCluster()inrun_pathfindR()(#45) - fixed save-related issue in
download_kegg_png()(#37, @rix133) - added the output data
RA_comparison_outputof pathfindR results on another RA-related dataset (GSE84074) - in
visualize_hsa_KEGG(), fixed the issue where >1 entrez ids were returned for a gene symbol (the first one is kept) - in
visualize_hsa_KEGG(), implemented a tryCatch to avoid any issues whenKEGGREST::color.pathway.by.objects()might fail (#28) - in
visualize_hsa_KEGG(), now limiting the number of genes passes ontoKEGGREST::color.pathway.by.objects()to < 60 (because the KEGG API now limits the number?) - changed default visualization in
term_gene_heatmap()(i.e. whengenes_dfis not provided) to binary colored heatmap (by default, "green" and "red", controlled bylowandhigh) by up-/down- regulation status - update the vignette "pathfindR Analysis for non-Homo-sapiens organisms" to reflect new data generation functions
get_pin_file()andget_gene_sets_list()and fixed a minor issue in the vignette (#46)
- Fixed corner case in
create_kappa_matrix()whenchanceis 1, the metric is turned into 0 - Fixed misused
class(.) == *incluster_graph_vis()
- Fixed error in DESCRIPTION: the Java version in SystemRequirements was corrected to "Java (>= 8.0)"
- The Java version is now checked
- Fixed behavior: when no input genes are present in the enriched hsa KEGG pathway, visualization of the pathway is now skipped
- Added the argument
max_to_plottovisualize_hsa_KEGG()and torun_pathfindR(). This argument controls the number of pathways to be visualized (default is NULL, i.e. no filter). This was implemented not to slow down the runtime ofrun_pathfindR()as downloading the png files is slow. - Fixed links to visualizations in
enriched_ters.Rmd
- Replaced most occurrences of "pathway" to "term". This was adapted because "term" reflects the utility of the package better. The enrichment and clustering approaches work with any kind of gene set data (be it pathway gene sets, gene ontology gene sets, motif gene sets etc.) Accordingly:
DESCRIPTIONwas updated- The functions
annotate_pathway_DEGs(),calculate_pw_scores(),cluster_pathways(),fuzzy_pw_clustering(),hierarchical_pw_clustering(),visualize_pw_interactions()andvisualize_pws()were renamed toannotate_term_DEGs(),score_terms(),cluster_enriched_terms(),fuzzy_term_clustering(),hierarchical_term_clustering(),visualize_term_interactions()andvisualize_terms()respectively - The Rmd template file for the report
enriched_pathways.Rmdwas renamed toenriched_terms.Rmd - All the Rmd template files for the report were updated
- Documentation of each function was updated accordingly
- Added the visualization function
term_gene_graph(), which creates a graph of enriched terms - involved genes - Made changes in
enrichment()andenrichment_analyses()to get enrichment results faster - Added the function
fetch_gene_set()for obtaining gene set data more easily - Terms in gene sets can now be filtered according to the number of genes a term contains (controlled by
min_gset_size,max_gset_sizeinfetch_gene_set()andrun_pathfindR()) - Added the argument
gaCrossoverduring active subnetwork search which controls the probability of a crossover in GA (default = 1, i.e. always perform crossover) - Added unit tests using
testthat - Updated all gene sets data
- Updated all RA example data
- The vignettes were updated
- Updated all PIN data
- Improved speed of kappa matrix calculation (
create_kappa_matrix()) - Added vignette for non-Homo-sapiens organisms
- Added Mus musculus (mmu) data:
mmu_kegg_genes&mmu_kegg_descriptions: mmu KEGG gene sets data- mmu STRING PIN
myeloma_input&myeloma_output: example mmu input and output data
- Added the STRING PIN (combined score >= 400)
- The argument
sig_gene_thrin subnetwork filtering viafilterActiveSnws()now serves the threshold proportion of significant genes in the active subnetwork. e.g., if there are 100 significant genes andsig_gene_thr = 0.03, subnetwork that contain at least 3 (100 x 0.03) significant genes will be accepted for further analysis - Removed
pathviewdependency by implementing colored pathway diagram visualization function usingKEGGRESTandKEGGgraph
- In
hierarchical_term_clustering(), redefined the distance measure as1 - kappa statistic - Fixed minor issue in
cluster_graph_vis()(during the calculations for additional node colors) - Removed title from graph visualization of hierarchical clustering in
cluster_graph_vis() - In
active_snw_search(), unnecessary warnings during active subnetwork search were removed - Fixed minor issue in
enrichment_chart(), supplying fuzzy clustered results no longer raises an error - Added new checks in
input_testing()andinput_processing()to ensure that both the initial input data frame and the processed input data frame for active subnetwork search contain at least 2 genes (to fix the corner case encountered in issue #17) - Fixed minor issue in
enrichment_chart(), ensuring that bubble sizes displayed in the legend (proportional to # of DEGs) are integers - In
enrichment_chart(), added the argumentsnum_bubbles(default is 4) to control number of bubbles displayed in the legend andeven_breaks(default isTRUE) to indicate if even increments of breaks are required - Updated the logo
- Minor fix in
term_gene_graph()(create the igraph object as an undirected graph for better auto layout) - Minor fix in
visualize_term_interactions(). The legend no longer displays "Non-input Active Snw. Genes" if they were not provided - The argument
human_genesinrun_pathfindR()andinput_processing()was renamed asconvert2alias - The gene symbols in the input data frame, the PIN and the gene sets are now turned into uppercase (for obtaining the best overlap)
- Added the argument
top_termstoenrichment_chart(), controlling the number top enriched terms to plot (default is 10) - Other minor bug/error fixes
- Separated the steps of the function
run_pathfindRinto individual functions:active_snw_search,enrichment_analyses,summarize_enrichment_results,annotate_pathway_DEGs,visualize_pws. - renamed the function
pathmapasvisualize_hsa_KEGG, updated the function to produce different visualizations for inputs with binary change values (ordered) and no change values (theinput_processingfunction, assigns a change value of 100 to all). - Created new the visualization function
visualize_pw_interactions, which creates PNG files visualizing the interactions (in the selected PIN) of genes involved in the given pathways. - Added new vignette, describing the step-by-step execution of the pathfindR workflow
- Changed clustering metric to kappa statistic, created the new clustering related functions
create_kappa_matrix,hierarchical_pw_clustering,fuzzy_pw_clusteringandcluster_pathways. - Implemented the new function
cluster_graph_visfor visualizing graph diagrams of clustering results.
- Fixed the bug where the arguments
score_quan_thrandsig_gene_thrforrun_pathfindRwere not being utilized. - in
run_pathfindR, added message at the end of run, reporting the number enriched pathways. - the function
run_pathfindRnow creates a variableorg_dirthat is the "path/to/original/working/directory".org_diris used in multiple functions to return to the original working directory if anything fails. This changes the previous behavior where if a function stopped with an error the directory was changed to "..", i.e. the parent directory. This change was adapted so that the user is returned to the original working directory if they supply a recursive output folder (output_dir, e.g. "./ALL_RESULTS/RESULT_A"). - in
input_processing, added the argumenthuman_genesto only perform alias symbol conversion when human gene symbols are provided. - Updated the Rmd files used to create the report HTML files - Added the data for
GO-All, all annotations in the GO database (BP+MF+CC) - Updated the vignette
pathfindR - An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworksto reflect the new functionalities.
- in the function
plot_scores, added the argumentlabel_casesto indicate whether or not to label the cases in the pathway scoring heatmap plot. Also added the argumentcase_control_titleswhich allows the user to change the default "Case" and "Control" headers. Also added the argumentslowandhighused to change the low and high end colors of the scoring color gradient. - in the function
plot_scores, reversed the color gradient to match the coloring scheme used by pathview (i.e. red for positive values, green for negative values) - minor change in
parseActiveSnwSearch, replacedscore_thrbyscore_quan_thr. This was done so that the scoring filter for active subnetworks could be performed based on the distribution of the current active subnetworks and not using a constant empirical score value threshold. - minor change in
parseActiveSnwSearch, increasedsig_gene_thrfrom 2 to 10 as we observed in most of the cases, this resulted in faster runs with comparable results. - in
choose_clusters, added the argumentp_val_thresholdto be used as p value threshold for filtering the enriched pathways prior to clustering.
- fixed issue related to the package
pathview.
- in the function
choose_clusters, added option to use pathway names instead of pathway ids when visualizing the clustering dendrogram and heatmap.
- Added the option to specify a custom gene set when using
run_pathfindR. For this, thegene_setsargument should be set to "Custom" andcustom_genesandcustom_pathwaysshould be provided.
- fixed minor bug in
calculate_pw_scoreswhere if there was one DEG, subsetting the experiment matrix failed - added if condition to check if there were DEGs in
calculate_pw_scores. If there is none, the pathway is skipped. - in
calculate_pw_scores, ifcasesare provided, the pathways are reordered before plotting the heat map and returning the matrix according to their activity incases. This way, "up" pathways are grouped together, same for "down" pathways. - in
calculate_pwd, if a pathway has perfect overlap with other pathways, change the correlation value with 1 instead of NA. - in
choose_clusters, ifresult_dfhas less than 3 pathways, do not perform clustering. run_pathfindRchecks whether the output directory (output_dir) already exists and if it exists, now appends "(1)" tooutput_dirand displays a warning message. This was implemented to prevent writing over existing results.- in run
run_pathfindR, recursive creation for the output directory (output_dir) is now supported. - in run
run_pathfindR, if no pathways are found, the function returns an empty data frame instead of raising an error.
-
Implemented the (per subject) pathway scoring function
calculate_pw_scoresand the function to plot the heatmap of pathway scores per subjectplot_scores. -
Added the
autoparameter tochoose_clusters. Whenauto == TRUE(default), the function chooses the optimal number of clusterskautomatically, as the value which maximizes the average silhouette width. It then returns a data frame with the cluster assignments and the representative/member statuses of each pathway. -
Added the
Fold_Enrichmentcolumn to the resulting data frame ofenrichment, and as a corollary to the resulting data frame ofrun_pathfindR. -
Added the option
bubbleto plot a bubble chart displaying the enrichment results inrun_pathfindRusing the helper functionenrichment_chart. To plot the bubble chart setbubble = TRUEinrun_pathfindRor useenrichment_chart(your_result_df).
-
Add the parameter
silent_optiontorun_pathfindR. Whensilent_option == TRUE(default), the console outputs during active subnetwork search are printed to a file named "console_out.txt". Ifsilent_option == FALSE, the output is printed on the screen. Default was set toTRUEbecause multiple console outputs are simultaneously printed when running in parallel. -
Added the
list_active_snw_genesparameter torun_pathfindR. Whenlist_active_snw_genes == TRUE, the function adds the columnnon_DEG_Active_Snw_Genes, which reports the non-DEG active subnetwork genes for the active subnetwork which was enriched for the given pathway with the lowest p value. -
Added the data
RA_clustered, which is the example output of the clustering workflow. -
In the function,
run_pathfindRadded the option to specify the argumentoutput_dirwhich specifies the directory to be created under the current working directory for storing the result HTML files.output_diris "pathfindR_Results" by default. -
run_pathfindRnow checks whether the output directory (output_dir) already exists and if it exists, stops and displays an error message. This was implemented to prevent writing over existing results. -
genes_table.htmlnow contains a second table displaying the input gene symbols for which there were no interactions in the PIN.
- Added the
gene_setsoption inrun_pathfindRto chose between different gene sets. Available gene sets areKEGG,Reactome,BioCartaand Gene Ontology gene sets (GO-BP,GO-CCandGO-MF) cluster_pathwaysautomatically recognizes the ID type and chooses the gene sets accordingly
- Fixed issue regarding p values < 1e-13. No active subnetworks were found when there were p values < 1e-13. These are now changed to 1e-13 in the function
input_processing - In
input_processing, genes for which no interactions are found in the PIN are now removed before active subnetwork search - Duplicated gene symbols no longer raise an error. If there are duplicated symbols, the lowest p value is chosen for each gene symbol in the function
input_processing - To prevent the formation of nested folders, by default and on errors, the function
run_pathfindRreturns to the user's working directory. - Citation information are now provided for our BioRxiv pre-print