Figure 3 Script

[RicardoRH96]

Hello, I have been following this paper since it was uploaded as a pre-print. First of all, congratulations for this amazing research! Could you please share the script for Figure 3? I am working with BDSKY data and would like to learn how to plot Re as you did, thanks in advance

[Koohoko]

Hi Ricardo,

Thanks for your email and interest in our paper! Would you please check if these codes https://github.com/HKU-SPH-COVID-19-Genomics-Consortium/HK-SARS-CoV-2-genomic-epidemiology/tree/master/scripts/BDSS can be helpful?

Best, Haogao

On Tue, Jun 7, 2022 at 1:50 AM Ricardo Rivero @.***> wrote:

Hello, I have been following this paper since it was uploaded as a pre-print. First of all, congratulations for this amazing research! Could you please share the script for Figure 3? I am working with BDSKY data and would like to learn how to plot Re as you did, thanks in advance

— Reply to this email directly, view it on GitHub https://github.com/HKU-SPH-COVID-19-Genomics-Consortium/HK-SARS-CoV-2-genomic-epidemiology/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2H6Z27DDJMUYJHFZRXCRDVNY27FANCNFSM5YADKNJA . You are receiving this because you are subscribed to this thread.Message ID: <HKU-SPH-COVID-19-Genomics-Consortium/HK-SARS-CoV-2-genomic-epidemiology/issues/1 @github.com>

[RicardoRH96]

Hi Haogao, indeed those codes work for me in order to visualize BDSKY results using skylinetools. But my interest is in knowing how to turn these plots into the visualization done by you in figure 3 where you overlapped Re over sequence number through time and the subsequent "beautification". I see you plot it as a ggplot object (ribbon+line) and transform the X axis into epiweeks. Also the way you plotted the phylogenetic tree on top is really interesting.

[tommy-lam]

Hi Ricardo. Some were done manually.

[RicardoRH96]

Thanks