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CONCERTDR 0.99.1

Bug fixes and improvements

  • process_signature_with_df() — gene coverage message now reflects topN: The "Found X/Y up-regulated genes" progress message previously reported overlap against the full signature gene list. It now sorts each direction by effect size, truncates to the topN genes actually passed to the scoring functions, and reports overlap against that subset. The denominator and percentage therefore match the genes that scoring methods such as XSum and XCos will use. The message also appends (top N per direction) to make the basis of the calculation explicit.

New features

  • Split-direction mode for extract_signature_zscores() and plot_signature_direction_tile_barcode(): Both functions now accept a split_direction argument (default FALSE).

    • In extract_signature_zscores(), setting split_direction = TRUE applies max_genes independently to the up-regulated (log2FC > 0) and down-regulated (log2FC < 0) gene sets, so each direction contributes up to max_genes columns (up to 2 * max_genes total). Genes within each group are ordered by effect size (most-positive first for up, most-negative first for down) before truncation.

    • In plot_signature_direction_tile_barcode(), setting split_direction = TRUE renders the heatmap as two side-by-side panels: up-regulated genes on the left and down-regulated genes on the right. A companion gap_width argument (default 5 mm) controls the gap between panels. Row clustering is performed on the full combined matrix so both panels display perturbations in the same order, enabling direct visual comparison of activation and suppression patterns within a single figure.

  • Reference-intersection highlighting in plot_signature_direction_tile_barcode(): When a reference_df is supplied, the function now computes the intersection of the signature genes with genes present in reference_df and visually distinguishes the two groups:

    • Genes not found in reference_df are shown in a muted silver-gray colour (#CCCCCC) with dimmed column labels, making the overlap immediately apparent without removing any genes from the display.

    • When cluster_cols = FALSE (default), all genes are kept in their original signature order (down-regulated first, then up-regulated); a cell_fun overlay is used to gray out non-intersecting columns without disturbing the column arrangement.

    • When cluster_cols = TRUE, the intersecting genes form a clustered panel and the non-intersecting genes are appended as a separate un-clustered panel in their original signature order (muted colour, labeled not in ref). When split_direction = TRUE is also active, this logic is applied within each direction sub-panel, yielding up to four panels in total (up-in-ref | up-not-in-ref | down-in-ref | down-not-in-ref).

CONCERTDR 0.99.0

Bioconductor submission

  • Fixed mailing list registration

CONCERTDR 0.5.0

New features

  • create_signature_from_gene_lists(): New convenience function to convert separate up-regulated and down-regulated gene lists into a signature data frame compatible with all CONCERTDR scoring functions. Up-regulated genes receive a default value of +1 and down-regulated genes receive -1.

  • Data frame input for signatures: process_signature_with_df(), extract_signature_zscores(), and plot_signature_direction_tile_barcode() now accept a data.frame (with Gene and log2FC columns) for the signature_file argument, in addition to the existing file-path input. This allows users to pass in-memory signature objects throughout the entire workflow without writing intermediate files.

  • Progress message for GCTX extraction: extract_cmap_data_from_siginfo() now prints a prominent notice before reading the GCTX file, letting users know the step may take a long time and should not be interrupted.

Documentation

  • Reorganised the workflow steps in all vignettes:
    • Steps 2 (Build reference matrix) and 3 (Prepare query signature) have been swapped so that users prepare their signature first.
    • Steps 4 (Annotate) and 5 (Visualise) have been merged into a single step.
  • Added examples for data-frame input and gene-list conversion in introduction.Rmd and signature_matching.Rmd.

CONCERTDR 0.4.0

New features

  • Added extract_signature_zscores() for pre-computing z-score matrices without rendering a plot, enabling reuse across repeated calls.
  • Added plot_signature_direction_tile_barcode() for publication-quality directional barcode heatmaps via ComplexHeatmap.
  • Added annotate_drug_results() producing four analysis-ready views: wetlab drug view, wetlab gene view, full technical table, and drug context summary.
  • Added subset_siginfo_beta() for interactive and non-interactive filtering of the CMap siginfo file.

Bug fixes and improvements

  • Replaced installed.packages() in .onLoad with requireNamespace() to comply with CRAN/Bioconductor startup function guidelines.
  • Removed non-ASCII characters from R source files.
  • Replaced sapply() with vapply() throughout for type-safe output.
  • Replaced 1:nrow(x) idiom with seq_len(nrow(x)) throughout.
  • Replaced \dontrun{} with \donttest{} in all man page examples.