Hi,
I am a beginner in bioinformatics. I have more than 500 genomes to analyze and I already got the results from Roary. I want to visualize these results by showing the tree compared to a matrix with the presence and absence of core and accessory genes. Roary provides us with roary_plots.py, which can achieve this. However, If I have hundreds of genomes, the plot will be a mess and nor very clear.
If there are any tips to make the tree look more clear in the cases of having hundreds of genomes, I'd be grateful to hear them.
Best,
Lingyu
Hello Lingyu,
I'm not sure if there is an optimal way to do it with roary_plots.py, since hundreds of genomes will still be many rows. Looking at the code of roary_plots.py, you should be able to increase the width of the tree to improve the clarity by changing the “colspan” parameter in the tree display. You can also improve the size and resolution of the image with the “figsize” and “dpi” parameters.
Best regards,
Adrian
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