plot_multisample_CNA: code error in missing setting the blank_genome

[qingjian1991]

Hi:

When use the plot_multisample_CNA() for plotting multi-regional CNAs, I found some errors in your codes

The original code is:
#line 62-66 #Default blank genome -- remove labels with label_chr = NA bl_genome = suppressMessages( CNAqc:::blank_genome(label_chr = NA) + labs(x = "", y = "") )

This code forgets to set some parameters. The corrected code may be:

bl_genome = suppressMessages(CNAqc:::blank_genome( ref = L[[1]]$reference_genome, chromosomes = chromosomes, label_chr = NA) + labs(x = "", y = ""))

In addition, I suggest adding some parameters in this function to control the output styles, like parameters of plot_segments as well as KARYO_colors and min_length_show ( the minimal length of chromosomes to show )

Yours sincerely,

Qingjian Chen

[caravagn]

Hi @qingjian1991

• are you suggesting we miss the reference? If yes I think you are correct.
• upgrades are indeed possible, only those 2 would be required in your opinion?

[qingjian1991]

Hi @caravagn

• are you suggesting we miss the reference? If yes I think you are correct.

Reply: Yes, the original code missed the reference.

• upgrades are indeed possible, only those 2 would be required in your opinion?

Reply: I only set the two parameters. In addition, users maybe want to show the total copy numbers, rather than Karyotypes. I think this set would be helpful for users.

Hi @qingjian1991

• are you suggesting we miss the reference? If yes I think you are correct.
• upgrades are indeed possible, only those 2 would be required in your opinion?

[caravagn]

Makes sense. Do add the options and open another PR for me to check, happy to accept if everything works.

[caravagn]

Thanks @qingjian1991