CHANGELOG.md

Changelog

Unreleased

cnplot package

• Clone names are set in the regular weight: the clone labels beside the integer-CN profile and the <label> (<pct>%) row-block labels on the heatmap. The CN key's CNA title is regular as well.
• BAF_LIM = (-0.01, 1.01): default limits for a BAF-like axis on [0, 1], exported from cnplot. The pad keeps points at exactly 0 or 1 off the spine while the ticks still run 0.0 to 1.0. Used by the gallery/README BAF row (ylim) and the RDR-vs-BAF scatter (xlim), which previously used (-0.05, 1.05) and (0, 1).
• Fonts are configured in one module, cnplot.cnplot_style: the family list (FONT_FAMILY), the embedding types (FONT_TYPE), the FS_* sizes, and apply_style(), which writes them into rcParams on import. No other module names a family, a size or an embedding type. FONT_FAMILY and apply_style are exported from cnplot.
• One type scale for every figure. The heatmap page, the integer-CN profile, the CN key, the proportion legends and the 2D scatter no longer carry their own literal font sizes (6 to 15 pt); they take FS_TICK, FS_LEGEND, FS_AXLABEL, FS_AXTITLE and FS_TITLE, and the same sizes are set as rc defaults on import so text drawn without an explicit size (a colorbar's ticks) follows. FS_ANNOT is new, for labels written on the data.
• Layout measured instead of assumed, so it holds at any font size:
  • the CN key labels each state (a,b) and wraps its groups onto further rows until the widest label fits under one swatch; it never shrinks the type or the notation;
  • plot_strip_legend stacks legends by their rendered height. Its entry_h argument is removed and gap defaults to half a legend line;
  • the heatmap colorbar grows until neighbouring tick labels clear each other, and the strip legends start to the right of its rendered tick labels;
  • the plot_heatmap_cnp title is anchored above the mesh rather than at a fixed figure height.
• Genome-axis labels are placed so they clear each other at the type scale:
  • chromosome names keep their rotation (60 degrees by default); names closer together than a line at that angle are nudged apart along the axis, and on an axes too narrow to hold them in one row, alternate crowded names go on a second row (chrname_tiers tells a layout which case applies);
  • in Mb mode an Mb label within a line of the previous one is left blank (its tick mark stays), the chromosome names under the Mb labels are offset in points rather than as a fraction of the axes, and on a stacked page only the last row labels its Mb ticks;
  • the gap between a row and the profile under it is sized in inches from the labels it holds (genome_label_room) by plot_scatter_1d_multisample and plot_heatmap_cnp, and plot_heatmap_cnp no longer opens the same gap between the profile and its key.
• The README gallery is drawn 20 in wide, the width the type scale assumes.
• FigureSaver.close() can be called twice on every supported matplotlib.
• Importing cnplot stops matplotlib's PDF backend storing rasterized layers as /Indexed palette images. With pdf.compression on, the backend converts any RGB raster of 256 or fewer colours to a palette and packs the indices at 1, 2 or 4 bits per pixel when the palette is small, which vector editors misread, so a copy-number raster opened in the wrong colours. Rasters are now written at 8 bits per component in DeviceRGB, still Flate-compressed. The hook is on PdfFile._writeImg, so it applies to every PDF the process writes, through FigureSaver, PdfPages or Figure.savefig. Rendered pixels are unchanged; a PDF holding such rasters is larger. This works around a known matplotlib bug, wrong colours when such a PDF is opened in Adobe Illustrator (matplotlib#27893), for which matplotlib has no setting; remove the hook once that is fixed upstream.
• FigureSaver no longer holds a whole-figure raster buffer per rasterized artist. matplotlib renders each rasterized artist into a buffer the size of the entire figure and passes the PDF backend a view of it, and the backend keeps every image until the file is finalized, so a multi-page PDF pinned n_artists * fig_w_in * fig_h_in * dpi^2 bytes until close. FigureSaver.savefig now copies each image on the way in, so only the cropped pixels are retained. Written output is byte-identical.

0.1.1

Backward-compatible additions; existing calls and output are unchanged.

cnplot package

• decorate_genome_axis gains mb_ticks / mb_tick_step: label x in Mb every mb_tick_step bp within each chromosome (reset per chromosome), with chromosome names drawn as compact off-axis text - the denser mode for genome-wide scatter QC. Plumbed through plot_scatter_1d, plot_scatter_1d_multisample, plot_heatmap, and plot_heatmap_cnp. Default off, 50Mb step; the Mb labels are rotated by rotation (default 60 degrees) so the dense ticks do not overlap.
• Version lives in the repo-root VERSION file: pyproject.toml builds from it (dynamic version = {file = "VERSION"}) and cnplot.__version__ reads it back, falling back to the installed metadata outside a source checkout. One edit per bump.
• GenomeAxis(region_bed=None): build one full-length region per chromosome from chrom_sizes, i.e. a plain whole-genome axis with no gaps, for callers that only have a sizes file.

0.1.0

First release of cnplot, the shared copy-number plotting library.

cnplot package

• GenomeAxis: a genome coordinate transform built from a region BED and chromosome sizes, mapping any bin table by (#CHR, START, END).
• Colormaps: get_cn_cmap, get_ascn_cmap, get_baf_cmap, get_log2rdr_cmap, get_mixcn_cmap, get_multiclass_cmap, set_palette.
• Integer copy-number profiles: plot_cnv_profile over the seg.ucn table.
• 1D genome scatter: plot_scatter_1d and the plot_scatter_1d_multisample builder, with hue/palette and an optional expected_df overlay.
• 2D RDR/BAF scatter: plot_scatter_2d (seaborn JointGrid) with copy-number landmarks.
• Single-cell heatmap: plot_heatmap / plot_heatmap_cnp with ordered categorical and posterior side strips and an optional value colorbar.