scaffold contig reorder

import time

import cooler

import trackc as tc

clr = cooler.Cooler("contig_bin_interaction.mcool::/resolutions/500000")

random contig order

fig, axs = tc.make_spec(figsize=(6, 6), width_ratios=[1], wspace=0.2)

mat = clr.matrix(balance=False)[:]
tc.pl.mapC(ax=axs[0], mat=mat, map_type="squ", symmetric=True)
chromstarts = [clr.extent(i)[0] for i in clr.chromnames]
_ = axs[0].set(yticks=chromstarts, yticklabels=clr.chromnames)
# tc.savefig('all_chrom_cmap.pdfx')

no max min range
maxrange: 36.0 minrange: 1.0

inside chrom/scaffold rearrange contig order or Orientation

chrom_contigs = reorder.query('Chromosome=="chr04"')
display(chrom_contigs)
order1 = chrom_contigs["region"].to_list()

import random

order2 = random.sample(order1, len(order1))

	Chromosome	Start	End	Order	Tag	Contig_ID	Contig_start	Contig_end	Orientation	base0_start	base0_end	region
57	chr04	1	81175125	1	W	ptg000018l	1	81175125	-	81175124	0	ptg000018l:81175124-0
59	chr04	81175226	168412693	3	W	ptg000008l	1	87237468	+	0	87237467	ptg000008l:0-87237467
61	chr04	168412794	172158802	5	W	ptg000031l	1	3746009	+	0	3746008	ptg000031l:0-3746008
63	chr04	172158903	183822856	7	W	ptg000044l	1	11663954	-	11663953	0	ptg000044l:11663953-0
65	chr04	183822957	314807117	9	W	ptg000006l	1	130984161	+	0	130984160	ptg000006l:0-130984160
67	chr04	314807218	315127496	11	W	ptg000056c	1	320279	-	320278	0	ptg000056c:320278-0
69	chr04	315127597	328337094	13	W	ptg000048l	1	13209498	+	0	13209497	ptg000048l:0-13209497
71	chr04	328337195	329026905	15	W	ptg000059l	1	689711	+	0	689710	ptg000059l:0-689710
73	chr04	329027006	330895159	17	W	ptg000047l	1	1868154	-	1868153	0	ptg000047l:1868153-0
75	chr04	330895260	332955347	19	W	ptg000068l	1	2060088	+	0	2060087	ptg000068l:0-2060087

start_time = time.time()
r1_mat = tc.tl.extractContactRegions(clr=clr, row_regions=order1)
r2_mat = tc.tl.extractContactRegions(clr=clr, row_regions=order2)
time.time() - start_time

ten = tc.tenon(figsize=(6, 1))
ten.add(pos="bottom", height=6)
ten.add(pos="bottom", height=3)
ten.add(pos="bottom", height=0.4)
ten.add(pos="bottom", height=3)


tc.pl.mapC(
    ax=ten.axs(0),
    mat=r1_mat.cmat,
    mat2=r2_mat.cmat,
    label=["chr4 contig order", "scaffold4 draft contig order"],
    cmap=["PuBu", tc.pa.fruitpunch],
    map_type="squ",
)

tc.pl.multi_scale_track(
    ten.axs(1), regions=order2, scale_adjust="Mb", intervals=7, tick_rotation=0
)

tc.pl.zoomin(
    ax=ten.axs(2),
    raw_regions=order2,
    zoomin_regions=order1,
    line_on=True,
    fill=True,
    alpha=0.5,
)

tc.pl.multi_scale_track(
    ten.axs(3), regions=order1, scale_adjust="Mb", intervals=7, tick_rotation=0
)


# tc.savefig('reorder_contig.pdf')

no max min range
maxrange: 243.0 minrange: 1.0
no max min range
maxrange: 243.0 minrange: 1.0