gcell.dna.track.Track

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gcell.dna.track.Track#

class gcell.dna.track.Track(chrom, start, end, assembly, tracks, normalize_factor=None, conv_size=50)[source]#

A class to represent and manipulate genomic track data.

This class handles genomic track data, including normalization, convolution, and visualization. It supports multiple tracks and provides methods for plotting, generating bedGraph and BigWig files.

Attributes

conv_size

Get the convolution window size.

Methods

generate_bedgraph(label, out_file)

Generate a bedGraph file for a specific track.

generate_bigwig(label, out_file)

Generate a BigWig file for a specific track.

get_local_iqr_peak(label[, min_length, ...])

Get local IQR peaks for a specific track.

plot_tracks([color_dict, gene_annot, ...])

Plot the convolved tracks and optionally add gene annotations.

plot_tracks_with_genebody([color_dict, ...])

Plot the tracks with detailed gene structure visualization.
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