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fix issues when plotting matrix close to the chr end #242

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Jun 4, 2020
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fix issues when plotting matrix close to the chr end #242

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6 changes: 3 additions & 3 deletions pygenometracks/tracks/HiCMatrixTrack.py
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Original file line number Diff line number Diff line change
Expand Up @@ -193,17 +193,17 @@ def plot(self, ax, chrom_region, region_start, region_end):
# get bin id of start and end of region in given chromosome
chr_start_id, chr_end_id = self.hic_ma.getChrBinRange(chrom_region)
chr_start = self.hic_ma.cut_intervals[chr_start_id][1]
chr_end = self.hic_ma.cut_intervals[chr_end_id - 1][1]
chr_end = self.hic_ma.cut_intervals[chr_end_id - 1][2]
start_bp = max(chr_start, region_start - self.properties['depth'])
end_bp = min(chr_end, region_end + self.properties['depth'])

idx, start_pos = list(zip(*[(idx, x[1]) for idx, x in
enumerate(self.hic_ma.cut_intervals)
if x[0] == chrom_region and x[1] >= start_bp and x[2] <= end_bp]))

idx = idx[0:-1]
# select only relevant matrix part
matrix = self.hic_ma.matrix[idx, :][:, idx]
# update the start_pos to add the last end:
start_pos = tuple(list(start_pos) + [self.hic_ma.cut_intervals[idx[-1]][2]])
# limit the 'depth' based on the length of the region being viewed

region_len = region_end - region_start
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