Good evening, I am lost trying to find a solution regarding my circos plot for comparative genomics.
I have a nucmer table that reports the whole genome alignment coordinates.
Below a subset of the table:
[S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [LEN R] [LEN Q] [COV R] [COV Q] [REFERENCE] [QUERY]
33089 48558 3881024 3896487 15470 15464 6940169 3934249 0.22 0.39 CP022024.1 contig_1
116330 123218 3796367 3803260 6889 6894 6940169 3934249 0.10 0.18 CP022024.1 contig_1
2360288 2369985 189419 199138 9698 9720 2546252 1384352 0.38 0.70 CP022030.1 contig_10
2375039 2380696 204161 209759 5658 5599 2546252 1384352 0.22 0.40 CP022030.1 contig_10
2380831 2389025 209897 218099 8195 8203 2546252 1384352 0.32 0.59 CP022030.1 contig_10
2460799 2467982 221610 228815 7184 7206 2546252 1384352 0.28 0.52 CP022030.1 contig_10
4439741 4445570 430927 436763 5830 5837 6940169 1177390 0.08 0.50 CP022024.1 contig_12
4498636 4506710 464390 472465 8075 8076 6940169 1177390 0.12 0.69 CP022024.1 contig_12
4528427 4553237 494202 518974 24811 24773 6940169 1177390 0.36 2.10 CP022024.1 contig_12
I did my fuction to create the circos.link:
def make_synteny_links(nucmer_coord, circos, all_forward = True,
highlight_ref_contig = [], highlight_qry_contig = [],
links_color = "grey", from_qry_highlighted_links_color = "green", from_ref_highlighted_links_color = "cyan"):
"""
Create the circos links based on the nucmer alignments.
If a specific contig/chromosome is provided (from reference or query genome) the link of this contig/chromosome is highlighted in a different color.
"""
found_reverse = False
for _, nc in nucmer_coord.iterrows():
# Set tuple for the reference genome
refgenome_contig = nc["REFERENCE"]
if (nc["S1"] < nc["E1"]) and all_forward:
ref_start, ref_end = nc["S1"], nc["E1"]
else:
ref_start, ref_end = nc["E1"], nc["S1"]
# Set tuple for the query genome
qrygenome_contig = nc["QUERY"]
if nc["S2"] < nc["E2"] and all_forward:
qry_start, qry_end = nc["S2"], nc["E2"]
else:
qry_start, qry_end = nc["E2"], nc["S2"]
region1 = (qrygenome_contig, qry_start, qry_end)
region2 = (refgenome_contig, ref_start, ref_end)
# Highlight contigs/chromosomes in the
if refgenome_contig in highlight_ref_contig:
# print(f"{refgenome_contig} - {highlight_ref_contig}")
color = from_ref_highlighted_links_color
# Highlight from strawberry to apple
elif qrygenome_contig in highlight_qry_contig:
color = from_qry_highlighted_links_color
else:
color = links_color
circos.link(region1, region2, color=color, r1=96, r2=96, allow_twist=False)
return circosHowever, in the Circos plot, some links remain twisted, despite attempts to fix the issue using my function, and although the entire genome alignment was already in the forward strand.
I hope you can help me.
Regards.
Good evening, I am lost trying to find a solution regarding my circos plot for comparative genomics.
I have a nucmer table that reports the whole genome alignment coordinates.
Below a subset of the table:
I did my fuction to create the circos.link:
However, in the Circos plot, some links remain twisted, despite attempts to fix the issue using my function, and although the entire genome alignment was already in the forward strand.
I hope you can help me.
Regards.