Generate actuation plots from fibertools pileup files with strand-aware coordinate handling.
fire-window creates ribbon plots showing FIRE (Fiber-seq Inferred Regulatory Elements) actuation levels across genomic regions. The tool reads tabix-indexed pileup files generated by fibertools and produces centered, multi-track visualizations with proper strand correction.
Make sure you have pixi installed.
Add the bin/ directory to your PATH to use fire-window from anywhere:
export PATH="/path/to/fire-window/bin:$PATH"Or run directly using the path:
/path/to/repo/bin/fire-window manifest.bed -o output.pdffire-window manifest.bed -o output.pdf [options]manifest.bed- Tab-separated manifest file with required columns:#chrom- chromosome/contig namestart- region start position (0-based)end- region end positioncenter- centered position for plottingpileup- path to tabix-indexed fibertools pileup BED filestrand- (optional) strand orientation (+or-); defaults to+
-o, --output- Output PDF file path (required)-t, --height-per-track- Height per track in inches (default: 1)-w, --width- Figure width in inches (default: 8)-c, --color- Color for the ribbon plot (default: darkred)-b, --highlight-bed- Optional BED file with regions to highlight (3-column: chrom, start, end)--highlight-color- Color for highlighted regions (default: darkorange)
Basic usage:
fire-window regions.bed -o actuation_plot.pdf -t 1.5 -w 10 -c "#8B0000"With highlighted regions:
fire-window regions.bed -o actuation_plot.pdf -b highlights.bed -c "#8B0000"The tool generates a PDF with:
- FIRE actuation levels (0-100%) shown as colored ribbon plots
- Optional highlighted regions shown as semi-transparent orange rectangles
- Vertical dashed line marking the alignment center
- Horizontal blue line indicating the region boundaries
- Separate facets for each region in the manifest
Format R code:
pixi run format