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Recent Releases of pathfindR

pathfindR - pathfindR 2.5.1

Minor Changes and Bug Fixes

  • fixed NA values in kappa matrix generation that will cause error as part of the latest igraph update (#227)

- R
Published by egeulgen 11 months ago

pathfindR - pathfindR 2.5.0

Major Changes

  • updated dependencies so that pathfindR depends on msigdbr (>= 24.1.0)
  • added the new db_species argument to the get_mgsigdb_gsets() data generation function

Minor Changes and Bug Fixes

  • fixed test assertions that will break as part of the latest ggplot2 update (#223)

- R
Published by egeulgen 12 months ago

pathfindR - pathfindR 2.4.2

Minor Changes and Bug Fixes

  • fixed a bug in visualize_KEGG_diagram() where ggkegg was raising an error (#214)

- R
Published by egeulgen over 1 year ago

pathfindR - pathfindR 2.4.1

Minor Changes and Bug Fixes

  • 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

- R
Published by egeulgen about 2 years ago

pathfindR - pathfindR 2.4.0

Major Changes

  • implemented a new color_kegg_pathway() function using ggkegg to create colored KEGG pathway ggplot objects (instead of using KEGGREST to obtain the colored PNG files, which no longer works #169)
  • renamed the visualize_hsa_KEGG function to visualize_KEGG_diagram() to reflect this is now able to handle KEGG pathway enrichment results from any organism
  • updated the visualize_terms(), visualize_term_interactions() and visualize_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 use ggkegg for fetching genes per pathway data
  • removed unneeded dependencies: magick, KEGGgraph and KEGGREST

Minor Changes and Bug Fixes

  • updated the get_biogrid_pin() function so that it can now determine the latest version and download/process it from BioGRID (via setting release = "latest", which is now the default behavior)

- R
Published by egeulgen about 2 years ago

pathfindR - pathfindR 2.3.1

Minor Changes and Bug Fixes

  • fixed a bug in the UpSet_plot() plot function regarding the interaction with ggupset package that was discovered in a reverse dependency check for ggplot2 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()

- R
Published by egeulgen over 2 years ago

pathfindR - pathfindR 2.3.0

Major Changes

  • reverted removal of create_HTML_report() so run_pathfindR() once again generates HTML reports

- R
Published by egeulgen over 2 years ago

pathfindR - pathfindR 2.2.0

Minor Changes and Bug Fixes

  • added the disable_parallel argument in active_snw_enrichment_wrapper() to be able to disable parallel runs via foreach
  • fixed the issue encountered on CentOS where forech wasn't loading pathfindR (#164)
  • fixed a CRAN error due to a package documentation issue (#172)
  • performed some refactoring and updated/improved all tests

- R
Published by egeulgen almost 3 years ago

pathfindR - pathfindR 2.1.0

Minor Changes

  • removed create_HTML_report() so run_pathfindR() no longer generates a HTML report

- R
Published by egeulgen about 3 years ago

pathfindR - pathfindR 2.0.1

Minor Changes

  • added the dir_for_report argument in the internal function create_HTML_report() to fix test issues on CRAN

- R
Published by egeulgen about 3 years ago

pathfindR - pathfindR 2.0.0

Major Changes

  • updated the java active subnetwork search component and added the seedForRandom argument in active_snw_search()to ensure reproducibility. By default behavior, in run_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 set output_dir to 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

Minor Changes

  • fixed a minor issue in return_pin_path() where the PIN was not properly read (#157)

- R
Published by egeulgen about 3 years ago

pathfindR - pathfindR 1.6.4

Minor Changes

  • 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) in color_kegg_pathway(), the default is now scale_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 in genes_df
  • added the sort_terms_by_p argument to the term_gene_heatmap() function to enable sorting of terms by 'lowest_p'
  • in visualization functions, made coloring of up-/down-regrulated genes consistent (#126)
  • added the vertex.label.cex and vertex.size.scaling arguments to cluster_graph_vis()
  • added the show_legend argument to visualize_term_interactions() to toggle the legend

- R
Published by egeulgen almost 4 years ago

pathfindR - pathfindR v1.6.3

Minor Changes

  • Fixed coloring issue in color_kegg_pathway()
  • In color_kegg_pathway() the default value for normalize_vals is now FALSE

- R
Published by egeulgen over 4 years ago

pathfindR - pathfindR v1.6.2

Major Changes

  • fixed an issue in get_kegg_gsets() where empty result was returned for some organisms due to an error in parsing (#72)

Minor changes and bug fixes

  • added repel = TRUE in term_gene_graph() and combined_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 to wget (now set to auto, 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(), swapped bg_color with fg_color due to an issue with KEGGREST
  • 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

- R
Published by egeulgen almost 5 years ago

pathfindR - pathfindR v1.6.1

Major Changes

  • In run_pathfindR(), the default iterations was set back to 10 (the default for all other v1.x)

- R
Published by egeulgen over 5 years ago

pathfindR - pathfindR v1.6.0

Major Changes

  • In run_pathfindR(), as "GR" (the default active subnetwork search method) provides nearly identical results in each iteration, the default iterations is 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

Minor changes and bug fixes

  • 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)

- R
Published by egeulgen over 5 years ago

pathfindR - pathfindR 1.6.0.9005

Major Changes

  • In run_pathfindR(), as "GR" (the default active subnetwork search method) provides nearly identical results in each iteration, the default iterations is set to 1
  • added the column 'support' (the proportion of active subnetworks leading to enrichment over all subnetworks) in the output

Minor changes and bug fixes

  • 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)

- R
Published by egeulgen over 5 years ago

pathfindR - pathfindR v1.5.1

Minor changes and bug fixes

  • 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)

- R
Published by egeulgen over 5 years ago

pathfindR - pathfindR 1.5.1.9001

  • 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)

- R
Published by egeulgen almost 6 years ago

pathfindR - pathfindR v1.5.0

Major Changes

  • created separate package pathfindR.data for 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() and combined_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. If genes_df is 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_gsets and cell_markers_descriptions

Minor changes and bug fixes

  • fixed an issue regarding parallel::makeCluster() in run_pathfindR() (#45)
  • fixed save-related issue in download_kegg_png() (#37, @rix133)
  • added the output data RA_comparison_output of 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 when KEGGREST::color.pathway.by.objects() might fail (#28)
  • in visualize_hsa_KEGG(), now limiting the number of genes passes onto KEGGREST::color.pathway.by.objects() to < 60 (because the KEGG API now limits the number?)
  • changed default visualization in term_gene_heatmap() (i.e. when genes_df is not provided) to binary colored heatmap (by default, "green" and "red", controlled by low and high) by up-/down- regulation status
  • update the vignette "pathfindR Analysis for non-Homo-sapiens organisms" to reflect new data generation functions get_pin_file() and get_gene_sets_list() and fixed a minor issue in the vignette (#46)

- R
Published by egeulgen almost 6 years ago

pathfindR - pathfindR 1.5.0.9010

  • minor changes before v1.5.0 release

- R
Published by egeulgen about 6 years ago

pathfindR - pathfindR 1.5.0.9009

  • implemented workaround for the makePSOCKcluster update issue in run_pathfindR()
  • implemented a fix for layout issue in combined_results_graph()

- R
Published by egeulgen about 6 years ago

pathfindR - pathfindR 1.5.0.9008

  • improved term_gene_heatmap()
  • fixed minor issues in term_gene_heatmap() and UpSet_plot()

- R
Published by egeulgen about 6 years ago

pathfindR - pathfindR 1.5.0.9007

  • added new visualization type for UpSet_plot()
  • fixed an issue with file naming on Windows in visualize_term_interactions()

- R
Published by egeulgen about 6 years ago

pathfindR - pathfindR 1.5.0.9006

fixed issue in term_gene_heatmap()

- R
Published by egeulgen about 6 years ago

pathfindR - pathfindR 1.5.0.9005

- R
Published by egeulgen about 6 years ago

pathfindR - pathfindR v1.4.2

Minor changes and bug fixes

  • Fixed corner case in create_kappa_matrix() when chance is 1, the metric is turned into 0
  • Fixed misused class(.) == * in cluster_graph_vis()

- R
Published by egeulgen over 6 years ago

pathfindR - pathfindR v1.4.1

Major Changes

  • Fixed error in DESCRIPTION: the Java version in SystemRequirements was corrected to "Java (>= 8.0)"
  • The Java version is now checked

Minor changes and bug fixes

  • Fixed behaviour: when no input genes are present in the enriched hsa KEGG pathway, visualization of the pathway is now skipped
  • Added the argument max_to_plot to visualize_hsa_KEGG() and to run_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 of run_pathfindR() as downloading the png files is slow.
  • Fixed links to visualizations in enriched_ters.Rmd

- R
Published by egeulgen over 6 years ago

pathfindR - pathfindR 1.4.0

Major Changes

  • 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:
    • DESCRIPTION was updated
    • The functions annotate_pathway_DEGs(), calculate_pw_scores(), cluster_pathways(), fuzzy_pw_clustering(), hierarchical_pw_clustering(), visualize_pw_interactions() and visualize_pws() were renamed to annotate_term_DEGs(), score_terms(), cluster_enriched_terms(), fuzzy_term_clustering(), hierarchical_term_clustering(), visualize_term_interactions() and visualize_terms() respectively
    • The Rmd template file for the report enriched_pathways.Rmd was renamed to enriched_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() and enrichment_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_size in fetch_gene_set() and run_pathfindR())
  • Added the argument gaCrossover during 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_thr in subnetwork filtering via filterActiveSnws() now serves the threshold proportion of significant genes in the active subnetwork. e.g., if there are 100 significant genes and sig_gene_thr = 0.03, subnetwork that contain at least 3 (100 x 0.03) significant genes will be accepted for further analysis
  • Removed pathview dependency by implementing colored pathway diagram visualization function using KEGGREST and KEGGgraph

Minor changes and bug fixes

  • In hierarchical_term_clustering(), redefined the distance measure as 1 - 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() and input_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 arguments num_bubbles (default is 4) to control number of bubbles displayed in the legend and even_breaks (default is TRUE) 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_genes in run_pathfindR() and input_processing() was renamed as convert2alias
  • 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_terms to enrichment_chart(), controlling the number top enriched terms to plot (default is 10)
  • Other minor bug/error fixes

- R
Published by egeulgen over 6 years ago

pathfindR - pathfindR 1.3.0

Major Changes

  • Separated the steps of the function run_pathfindR into individual functions: active_snw_search, enrichment_analyses, summarize_enrichment_results, annotate_pathway_DEGs, visualize_pws.
  • renamed the function pathmap as visualize_hsa_KEGG, updated the function to produce different visualizations for inputs with binary change values (ordered) and no change values (the input_processing function, 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_clustering and cluster_pathways.
  • Implemented the new function cluster_graph_vis for visualing graph diagrams of clustering results.

Minor changes and bug fixes

  • Fixed the bug where the arguments score_quan_thr and sig_gene_thr for run_pathfindR were not being utilized.
  • in run_pathfindR, added message at the end of run, reporting the number enriched pathways.
  • the function run_pathfindR now creates a variable org_dir that is the "path/to/original/working/directory". org_dir is used in multiple funtions 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. "./ALLRESULTS/RESULTA").
  • in input_processing, added the argument human_genes to 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 Subnetworks to reflect the new functionalities.

- R
Published by egeulgen over 7 years ago