About HIC Plot

[linyuiz]

I couldn't find parameters for setting image dimensions（height and width）in the help documentation: https://wangyibin.github.io/CPhasing/latest/zh/CLI/plot/#parameters-of-plot. Additionally, for genomes with smaller chromosomes like mine, I can only use --no-ticks to prevent overlapping chromosome labels on the left, but I still want to retain the genome size (MB) scale at the bottom. What should I do?

[linyuiz]

Another question: Why is there no black border in the drawn image when I clearly set --add-hap-border?

cphasing plot -a rawname.agp -m Bam.q${mapq}.q0.10k.cool -o hic_plot.png -bs 500k -oc --dpi 150 -t 60 --whitered --balanced --no-ticks --no-lines --add-hap-border

Chr32g1	1	4006523	1	W	chr32	1	4006523	+
Chr33g1	1	5359772	1	W	chr33	1	5359772	+
Chr34g1	1	4119900	1	W	chr34	1	4119900	+
Chr35g1	1	3946276	1	W	chr35	1	3946276	+
Chr36g1	1	3849410	1	W	chr36	1	3849410	+
Chr37g1	1	4528314	1	W	chr37	1	4528314	+
Chr38g1	1	7067386	1	W	chr38	1	7067386	+
Chr39g1	1	30689022	1	W	chrW	1	30689022	+
Chr40g1	1	85815802	1	W	chrZ	1	85815802	+

My documents clearly meet this format:

--hap-pattern                default: (Chr\d+)g(\d+)

Is it mandatory to have both g1 and g2, or is having only g1 acceptable?