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Change URL to use DOI
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nickjcroucher committed Sep 14, 2023
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Expand Up @@ -97,7 +97,7 @@ These options provide flexibility with regard to the labelling of different comp

### Example

Using files from the associated [FigShare repository](https://figshare.com/account/projects/130637/articles/24117117), we can replicate the analysis shown in [Kwun, Ion, Cheng *et al*](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01147-2) with the command:
Using files from the associated [FigShare repository](dx.doi.org/10.6084/m9.figshare.24117117), we can replicate the analysis shown in [Kwun, Ion, Cheng *et al*](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01147-2) with the command:

```
plot_gubbins.R --tree serotype_3.tre --rec serotype_3_recombination.gff --annotation serotype_3_annotation.gff --meta serotype_3_metadata.csv --max-branch-length 500 --clades serotype_3_clades.csv --markup serotype_3_markup.csv --legend-height 0.35 --tree-axis-expansion 30 --markup-height 0.1 --heatmap-x-nudge 0.05 --heatmap-y-nudge -0.05 --output serotype_3.png
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