seg_bar_height + segment_bar_height, "darkorange")
# check overlaps of contigs and adjust heights accordingly
contig_height_shifts = vu.set_contig_height_shifts(contig_placements,
contig_list, -bar_width)
# plot contigs cmap
plot_cmap_track(contig_placements,
total_length,
seg_bar_height + contig_bar_height,
"cornflowerblue",
seg_id_labels=True)
# plot alignments
plot_alignment(contig_placements, path_seg_placements, total_length)
imputed_status = vu.imputed_status_from_aln(aln_vect, len(path))
print("RH", ref_bar_height, "BW", bar_width)
plot_ref_genome(ref_placements, path, total_length, segSeqD, imputed_status,
args.label_segs, args.color_map, gene_set)
if args.graph:
plot_bpg_connection(ref_placements, prev_seg_index_is_adj, bpg_dict,
seg_end_pos_d)
#ax.set_xlim(-(seg_bar_height+1.25), (seg_bar_height+1.25))
#ax.set_ylim(-(seg_bar_height+1.25), (seg_bar_height+1.25))
chrom_set = set()
for i in path:
chrom_set.add(segSeqD[i[0]][0])
plot_cmap_track(cycle_seg_placements, total_length,
outer_bar + segment_bar_height, "darkorange")
# check overlaps of contigs and adjust heights accordingly
contig_height_shifts = vu.set_contig_height_shifts(contig_placements,
contig_list)
# plot contigs
plot_cmap_track(contig_placements,
total_length,
outer_bar + contig_bar_height,
"cornflowerblue",
seg_id_labels=True)
# plot alignments
plot_alignment(contig_placements, cycle_seg_placements, total_length)
imputed_status = vu.imputed_status_from_aln(aln_vect, len(cycle))
plot_ref_genome(ref_placements, cycle, total_length, segSeqD, imputed_status,
args.label_segs, gene_set)
if args.graph:
plot_bpg_connection(ref_placements, cycle, total_length,
prev_seg_index_is_adj, bpg_dict, seg_end_pos_d)
ax.set_xlim(-(outer_bar + 1.25), (outer_bar + 1.25))
ax.set_ylim(-(outer_bar + 2.5), (outer_bar + 2.5))
chrom_set = set()
for i in cycle:
chrom_set.add(segSeqD[i[0]][0])
sorted_chrom = sorted(chrom_set, key=lambda x: x.rsplit("chr")[-1])
