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README.md

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A comprehensive example of pyGenomeTracks can be found as part of our automatic testing.
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Note, that pyGenome tracks also allows the combination of multiple tracks into one using the parameter: `overlay previous=yes` or `overlay previous=share-y`.
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Note, that pyGenome tracks also allows the combination of multiple tracks into one using the parameter: `overlay_previous=yes` or `overlay_previous=share-y`.
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In the second option the y-axis of the tracks that overlays is the same as the track being overlay. Multiple tracks can be overlay together.
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![pyGenomeTracks example](./pygenometracks/tests/test_data/master_plot.png)
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In these examples is where the overlay tracks are more useful. Notice that any track can be overlay over a Hi-C matrix. Most useful is to overlay TADs or to overlay links using the `triangles` option
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that will point in the Hi-C matrix the pixel with the link contact. When overlaying links and TADs is useful to set `overlay previous=share-y` such that the two tracks match the positions. This is not
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that will point in the Hi-C matrix the pixel with the link contact. When overlaying links and TADs is useful to set `overlay_previous=share-y` such that the two tracks match the positions. This is not
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required when overlying other type of data like a bigwig file that has a different y-scale.
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![pyGenomeTracks example](./pygenometracks/tests/test_data/master_plot_hic.png)

examples/bigwig_with_genes.ini

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title = genes
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fontsize = 10
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file_type = bed
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gene rows = 10
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gene_rows = 10
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examples/bigwig_with_genes_and_vlines.ini

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title = genes
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fontsize = 10
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file_type = bed
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gene rows = 10
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gene_rows = 10
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[x-axis]
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fontsize=10

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