Changelog

Source: NEWS.md

MotrpacRatTraining6mo 1.6.5 (2023-11-08)

• Point to development version of RCy3 from GitHub to avoid R-CMD check error RCy3: Can't install dependency uchardet.
• Install plotrix from GitHub instead of CRAN to avoid R-CMD check warning Requires (indirectly) orphaned package: ‘plotrix’. CRAN has marked plotrix as orphaned. plotrix is a dependency for mutoss, which is a dependency for metap.
• Increment required MotrpacRatTraining6moData version.

MotrpacRatTraining6mo 1.6.4 (2023-06-02)

• Bug fix in transcript_timewise_da() to run with limited contrasts when tissue="VENACV".

MotrpacRatTraining6mo 1.6.3 (2023-04-28)

• Create a new tag to associate with Zenodo.

MotrpacRatTraining6mo 1.6.2 (2023-03-09)

• Bug fix in atac_timewise_da() and atac_training_da() when n_features = Inf.

MotrpacRatTraining6mo 1.6.1 (2023-02-05)

• Accommodate RefMet IDs as feature IDs in plot_feature_normalized_data() and plot_feature_logfc().
  
• Pass the user-supplied version of the feature identifier when plot_feature_logfc() is called within plot_feature_normalized_data().

MotrpacRatTraining6mo 1.6.0 (2023-01-26)

• Add functions for GSEA and PTM-SEA: ssGSEA2_wrapper(), prepare_gsea_input(), prepare_ptmsea_input(), find_flanks(), load_uniprot_human_fasta()
  
• Add extract_top_trajectories() function.

MotrpacRatTraining6mo 1.5.2 (2023-01-20)

• For enrichment_network_vis() with argument return_html=TRUE, don’t require GNU sed.

MotrpacRatTraining6mo 1.5.1 (2023-01-19)

• In enrichment_network_vis(), include pathway names in determination of node labels.
  
• In enrichment_network_vis(), use MotrpacRatTraining6moData::FEATURE_TO_GENE_FILT as feature_to_gene default instead of the unfiltered version.
  
• Add more details to enrichment_network_vis() docs.

MotrpacRatTraining6mo 1.5.0 (2023-01-18)

• Add load_feature_annotation().
  
• Add counts argument to transcript_normalize_counts() and atac_normalize_counts() to allow user-supplied data.
  
• Add tissues, assays, and cluster arguments to enrichment_network_vis() to provide an alternate way for users to specify results from MotrpacRatTraining6moData::GRAPH_PW_ENRICH.
  
• Add tests for enrichment_network_vis().
  
• Use signif() instead of round() to display values in plot titles.
• Add note about reproducibility issues to documentation for transcript_normalize_counts().
  
• Move MotrpacRatTraining6moData from Imports to Depends. This means MotrpacRatTraining6moData is also attached (not just loaded) when MotrpacRatTraining6mo is attached.
  
• Replace fetch_object(name_as_string) with .get, which internally uses get(name_as_string, envir=as.environment("package:MotrpacRatTraining6moData")).
  
• Change URLs for load_methyl_feature_annotation() and load_atac_feature_annotation().
  
• Fix bug in plot_feature_logfc() that prevented epigenetic features from being plotted.
  
• Speed up plot_feature_logfc() for differential epigenetic features.
  
• In get_rdata_from_url(), calculate log fold-change standard errors for METHYL differential analysis results: logFC_se = logFC/zscore

MotrpacRatTraining6mo 1.4.3 (2023-01-06)

• In plot_feature_normalized_data() and plot_feature_logfc(), handle input features that don’t exist in the data.

MotrpacRatTraining6mo 1.4.2 (2023-01-06)

• Dodge points in plot_feature_normalized_data() and plot_feature_logfc() for readability.
  
• Make plot_feature_normalized_data() and plot_feature_logfc() more accommodating of features with multiple measurements.
  
• Add add_adj_p parameter to plot_feature_normalized_data().
  
• Add return_data parameter to plot_feature_logfc().
• Return NULL instead of error if data doesn’t exist for plotting plot_feature_normalized_data() in loops.

MotrpacRatTraining6mo 1.4.1 (2023-01-05)

• Fix custom_cluster_pathway_enrichment() to accept a list of lists as input.
• Use filtered feature-to-gene map to perform pathway enrichment.
• In cluster_pathway_enrichment(), remove pathway enrichments driven by a single gene for consistency with the landscape paper.

MotrpacRatTraining6mo 1.4.0 (2023-01-05)

• Add gene_pathway_enrichment() (wrapper for gprofiler2::gost()).
• Add example to “Get Started” vignette.

MotrpacRatTraining6mo 1.3.0 (2023-01-04)

• Add df_to_numeric() to easily format data frames.
• Add plot_feature_normalized_data() to plot normalized sample-level data for a single feature.
• Add plot_feature_logfc() to plot differential analysis results for a single feature.
• Add more examples and screenshots to the “Get Started” vignette.

MotrpacRatTraining6mo 1.2.0 (2022-12-27)

• Add functions to perform meta-analysis and meta-regression of redundant metabolites.
• Add load_training_da() to load training summary statistics from GSC.
  
• Retain order of input vial labels in result of viallabel_to_pid().

MotrpacRatTraining6mo 1.1.1 (2022-11-09)

• Use MotrpacRatTraining6moData::TRAINING_REGULATED_NORM_DATA and add a training_regulated_only argument to speed up plot_feature_trajectories()
• Fix bugs in get_tree_plot_for_tissue() and get_trajectory_sizes_from_edge_sets()
• Add scale argument to call_pca_outliers() (default TRUE)
  
• Set default values for arguments plot and verbose in call_pca_outliers() (default TRUE)

MotrpacRatTraining6mo 1.1.0 (2022-10-10)

• Add atac_call_outliers()
• Bug fix in atac_prep_data()

MotrpacRatTraining6mo 1.0.2 (2022-10-08)

• Use a hashmap to speed up calculation of similarity scores in enrichment_network_viz() (thanks, Jay Yu)
• Improve visInteraction settings in enrichment_network_viz(), i.e., show edges on zoom and slow down zoom
• Don’t run memory-intensive examples and vignette code blocks to prevent GitHub Actions OOM error

MotrpacRatTraining6mo 1.0.1 (2022-09-21)

• Bug fixes in transcript_timewise_da() and transcript_prep_data()
  
• Keep examples from printing too much output
  
• Rename tutorial.Rmd to MotrpacRatTraining6mo
  
• Add @keywords internal to functions that are not exported

MotrpacRatTraining6mo 1.0.0 (2022-09-20)

First release