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How to Customise the Forest Plots?

A detailed guide to all the customisation options available for refining your forest plot, including filters, panel options, and dataset highlighting.

The default plot can be refined using various options:


1. Filters

  • Haplotype reference panel (default 1000G).
  • P-value threshold (default 5e-4) – only studies where the query variant has a P-value below the threshold will be displayed. P-value threshold units can be switched to a -log10 scale using the ‘-log10’ option next to the P-value threshold box.
  • Imputation info threshold (inclusive) (default 0.8) – If the variant has been imputed by Genomics, studies where the variant imputation info score is less than this threshold will be filtered out. Range from 0 (plot all variants) to 1.

2. Top panel options


  • Minimum beta (default -0.4) – Change the lower beta cut-off. Any study with a beta below this value will be clipped in the plot area.
  • Maximum beta (default 0.4) – Change the upper beta cut-off. Any study with a beta above this value will be clipped in the plot area. 
  • Use logistic scale for beta – Beta values are log2 transformed prior to plotting.
  • Flip variant direction – The Y axis of the forest plot is inverted, equivalent to flipping the reference and alternate alleles.

Figure 3: The top panel customisation options.



Note: If the error bars do not appear to be symmetrical or the point estimate of the beta for one or more studies is not showing, adjust the minimum and maximum beta values in the options panel. Studies with a beta or 95% confidence interval will be cropped at this value.


3. Phenotypic categories

  • Group traits by phenotypic categories – Select/deselect the checkbox to turn this feature on/off. This enables or disables the grouping of studies by phenotypic category. Each specific category can also be toggled on/off by clicking on the category.

4. eQTLs

Include cis-eQTLs – Click the checkbox to toggle on/off. Enables or disables display of eQTL datasets.

Restrict to genes – Filter eQTL genes by gene name or ensemble gene ID.


5. Highlight datasets

Highlight datasets – Enter a study name or matching phenotype to create a new forest plot above the default plot. Only manually specified studies will appear in this plot.

Sort by p-value – Sort studies in the manual plot from ‘Highlight datasets’ by P-value. 

Sort by input order – Sort studies in the manual plot from ‘Highlight datasets’ by the order they were entered.

 

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Next: Variant View - Frequently Asked Questions.