Changelog

Source: NEWS.md

clover 0.0.0.9000

• plot_tRNA_structure() gains sprinzl_coords and trna_id parameters. When sprinzl_coords is provided, position columns in modifications, outlines, text_colors, and linkages are interpreted as Sprinzl labels and converted to 1-based sequence positions automatically (#20).

• compute_bcerror_delta() computes per-position differences in base-calling error rates between two conditions from a summarized bcerror tibble.

• prep_mod_heatmap() prepares bcerror delta data for plot_mod_heatmap() by joining Sprinzl coordinates, annotating known modifications, and shortening tRNA labels.

• identity_elements() returns experimentally validated tRNA aminoacylation identity elements (determinants and antideterminants) for a given organism, based on Giege & Eriani (2023). Use identity_organisms() to list supported organisms.

• map_identity_to_trna() converts Sprinzl-numbered identity elements to 1-based sequence positions for a specific tRNA, enabling overlay on plot_tRNA_structure() via the outlines parameter.

• plot_identity_panel() arranges multiple tRNA cloverleaf structures side by side in a single SVG, each annotated with aminoacylation identity elements colored by strength (red = strong, blue = weak).

• plot_identity_structure() generates a single tRNA cloverleaf structure SVG with identity element outlines, automatically mapping Sprinzl positions to sequence coordinates.

• structure_html() wraps a tRNA structure SVG in a centering <div> and returns an htmltools::HTML object, simplifying embedding in R Markdown and Quarto documents.

• filter_linkages() filters odds ratio data by p-value, observation count, and log odds ratio magnitude, returning a tibble ready for the linkages parameter of plot_tRNA_structure().

• plot_tRNA_structure() now accepts odds ratio tibbles directly as linkages input: if a log_odds_ratio column is present and value is not, it is automatically used as the arc value.

• plot_tRNA_structure() now draws a 3’ amino acid label (e.g., “Glu”) connected by a line to the terminal nucleotide, and position markers every 10 nucleotides around the cloverleaf. Position markers can be disabled with position_markers = FALSE.

• plot_tRNA_structure() now centers modification circles, outline circles, and linkage arcs on the visual center of nucleotide characters instead of the text baseline position.

• plot_tRNA_structure() overlays modification highlights and circuit linkage arcs on tRNA cloverleaf secondary structure SVGs. Use structure_organisms() and structure_trnas() to list bundled structures. Base SVGs are generated offline from gtRNAdb data via R2R.

• structure_to_png() converts a tRNA structure SVG to PNG format. Requires the rsvg package.

• plot_tRNA_structure() linkage arcs now route outward from the structure centroid instead of using a fixed perpendicular offset, avoiding arcs that cut through the interior. Overlapping arcs are assigned to separate lanes for visual clarity. Arc color encodes sign (blue for exclusive, vermillion for co-occurring) and stroke width encodes magnitude of the value. The legend updates to show bidirectional entries when both positive and negative values are present.

• Column naming is now standardized across the package: charging data and DESeq2 results use ref instead of tRNA for the tRNA reference name, and Sprinzl coordinates use pos instead of seq_index for the 1-based position in the tRNA body. The default lab_col parameter in plot_volcano(), plot_abundance_charging(), and tabulate_deseq() changed from "tRNA" to "ref". read_bcerror() now returns ref as character instead of factor.

• New color palette functions aa_colors() and charging_colors() provide named color vectors for amino acids and tRNA charging states.

• New statistical utility functions calc_fold_change(), cohens_d(), propagate_error_ratio(), and propagate_error_diff() for common tRNA analysis calculations.

• New trna_regions() returns a named list mapping canonical tRNA structural region names to Sprinzl position integers.

• aggregate_or_isodecoder() collapses per-gene odds ratios to isodecoder level by averaging across gene copies.

• build_or_network() constructs a tidygraph network from pairwise odds ratio or ROR data, with node centrality metrics.

• calculate_rewiring_scores() summarizes per-isodecoder rewiring magnitude from a ROR matrix.

• clean_odds_ratios() prepares odds ratio data for downstream analysis by capping infinite log odds ratio values.

• compute_ror_isodecoder() compares isodecoder-level odds ratios between two conditions with z-score significance testing.

• perform_pcoa() runs classical multidimensional scaling on a rewiring matrix for dimensionality reduction.

• plot_arc_diagram() creates a circular arc diagram from a tidygraph network built by build_or_network().

• plot_mod_heatmap() gains cluster_threshold to filter low-magnitude noise before clustering, fill_name and fill_breaks to customize the legend title and breaks, and improved caption styling with plot.caption.position = "plot".

• plot_mod_heatmap() gains new parameters for annotated heatmaps: label_col overlays text labels on tiles, highlight_col adds dot markers at selected cells, and group_col enables group-aware clustering with divider lines between groups. A caption parameter adds explanatory text below the plot.

• plot_mod_landscape() creates stacked multi-metric profile plots along the tRNA sequence, with optional structural region shading and Sprinzl position secondary axis. Uses patchwork for panel layout.

• plot_pcoa_rewiring() creates a scatter plot of PCoA coordinates colored by rewiring magnitude and labeled with top isodecoders.

• prepare_rewiring_matrix() builds a wide matrix from isodecoder-level relative odds ratios suitable for PCoA analysis.

• plot_abundance_charging() creates a scatter plot comparing tRNA abundance changes (from DESeq2) with charging ratio changes, with significant points colored by quadrant and labeled with ggrepel.

• plot_bcerror_profile() plots per-position base-calling error rates as a faceted line plot, with optional modification position overlay.

• plot_charging_diffs() creates a dot plot with error bars showing per-tRNA charging ratio differences between conditions.

• plot_chord_or() and plot_chord_ror() now convert positions from seq_index to Sprinzl labels when sprinzl_coords is provided, display all tRNA positions as sectors for structural context, and add annotation rings for structural region, reference nucleotide, and modification positions (via new mods parameter). Sectors now have equal widths for consistent visual comparison, a chord color legend is displayed, and default significance cutoffs are tighter (or_cutoff = 1.0, p_cutoff = 0.01, min_obs = 100) to reduce visual clutter.

• compute_charging_diffs() compares per-tRNA charging ratios between two conditions, returning mean ratios, standard errors, and the between-condition difference with propagated SE.

• compute_odds_ratios() now uses a C++ implementation (via cpp11) for the pairwise Fisher’s exact test inner loop, dramatically improving performance on large datasets. The odds ratio is now computed as the sample odds ratio with Haldane correction for zero cells, rather than the conditional MLE.

• fetch_modomics_mods() downloads tRNA modification annotations from the MODOMICS database and maps them onto reference sequences using pairwise alignment (#11).

• modomics_mods() maps MODOMICS tRNA modifications onto reference sequences using bundled data, eliminating the need for internet access. Use modomics_organisms() to list organisms with cached data. Falls back to fetch_modomics_mods() for unsupported organisms (#11).

• plot_volcano() creates a labeled volcano plot from tidy_deseq_results() output, with significant points highlighted and labeled using ggrepel.

• tabulate_deseq() creates a formatted gt table of the top significant tRNAs from tidy_deseq_results() output, sorted by p-value. The table now includes zebra striping, search, column sorting, and pagination.

• Initial CRAN submission.