pyGenomeTracks

Usage

This tool takes various types of tracks as input:

• Hi-C tracks:

  • TAD vizualisation: corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's hicPlotMatrix instructions. Boundaries file can used, which is the output of HiCExplorer's hicFindTADs in bed format. If selected, TADs will be drawn directly on the contact heatmap.
  • TAD score: display TAD seperation score computed by HiCExplorer's hicFindTADs.

• Chromatin states: display blocks of different colors following a bed file.
• Gene track / Bed Track: display genes or annotations in bed/gtf files. Labels like gene names can be toggled on or off.
• Link track: display links (pair of coordinates) as arcs, triangles or loops.
• NarrowPeak track: display narrowPeak (encode format) as boxes or as curve (reconstructed peak).
• Bigwig track: generic bigwig track plotting.
• Bedgraph track: generic bedgraph track plotting.
• Bedgraph matrix track is used to specifically plot bm files computed by HiCExplorer's hicFindTADs (TAD seperation scores).
• Vlines: vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's hicFindTADs.
• Vhighlight: vertical rectangles drawn on top of all tracks following a bed file. It is used as a visual support to highlight some regions.
• Hlines: horizontal lines drawn either by themselves or on top of other tracks.
• Spacer: Add some space between two tracks.
• X-axis: Plot x-axis scale wherever you want.
• Scale bar track: Plot scale bar.
• Fasta track: Display sequences from fasta.
• Maf track: Display alignments from maf.

For each track, parameters for the color, the width or the font size can be defined.

Output

Here are two example plots with the different tracks you can use (on the right, you have the vlines and vhighlight which have been used):