Ordering clonotypes per sample, and colour scheme using trackClonotypes about immunarch

[EugeneRumynskiy]

Hello @ssudhaman !

1. We need a data sample and a full code of the R script you are running. Without this things we can't reproduce the problem.

2. As I know, there isn't. But if you'll describe the problem in a bit more detailed way we might give an advise how to overcome it.

[vadimnazarov]

Hi @ssudhaman
in the latest 0.5.4 release we added a functionality to re-order samples. Feel free to check https://immunarch.com/articles/web_only/v8_tracking.html for more details. In short, you can provide an .order argument to the track Clonotypes function with sample indices to change the order of samples at the plot.

In order to change colour palette, you can use ColorBrewer palettes:

# tc - an output from trackClonotypes
vis(tc) + scale_fill_brewer(palette = "Spectral")

[ssudhaman]

Fantastic, thank you!

On Wed, Dec 4, 2019 at 9:07 AM Vadim Nazarov ***@***.***> wrote: Hi @ssudhaman <https://github.com/ssudhaman> in the latest 0.5.4 release we added a functionality to re-order samples. Feel free to check https://immunarch.com/articles/web_only/v8_tracking.html for more details. In short, you can provide an .order argument to the track Clonotypes function with sample indices to change the order of samples at the plot. In order to change colour palette, you can use ColorBrewer palettes: # tc - an output from trackClonotypes vis(tc) + scale_fill_brewer(palette = "Spectral") — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#15?email_source=notifications&email_token=AL5VHEAAIC64Z354ERS4FB3QW62SFA5CNFSM4IOY2JH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEF5EFGY#issuecomment-561660571>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AL5VHEB4AD56MBDG5DEDWXTQW62SFANCNFSM4IOY2JHQ> .

-- *Sumedha Sudhaman, PhD* *Research Fellow- SickKids, Toronto* *Mobile: [phone] **| Skype id: sumedhasudhaman*

[EugeneRumynskiy]

@ssudhaman How it's going? I'am closing the issue. If you have any questions or unresolved problems please let us know.

[ZJURenyi]

Hi EugeneRumynskiy,

Would it be possile to also add .order argument to vis(), when plotting diversity?

div_chao <- repDiversity(TCRα$data, "chao1")
vis(div_chao, .order=c(2,1))

The .order above seems cannot change the sample order.

Thank you!