TrumpetPlots is an R package to visualize the effect size of risk variants across the allele frequency spectrum.

For more information about Trumpet plots and to cite our work, visit our preprint Trumpet plots: Visualizing The Relationship Between Allele Frequency And Effect Size In Genetic Association Studies

To install, please install the “devtools” R package, then run

`devtools::install_git("https://gitlab.com/JuditGG/trumpetplots.git")`

The function trumpets only requires a text file as input, containing association results. Please indicate the column names of the input dataset using the following arguments:

`dataset`

: Input text file with genetic association results. Columns required are rsID, freq, A1_beta, Analysis and Gene.`rsID`

: (required) Single Nucleotide Polymorphism (SNP) name.`freq`

: (required) allele frequency of effect SNP.`A1_beta`

: (required) risk allele effect size.`Analysis`

: (optional) adds colour to the type of analysis (e.g. GWAS, Sequencing).`Gene`

: (optional) Candidate gene name (can be empty).`calculate_power`

: (TRUE/FALSE) Calculate power curves. Choose TRUE to add power curves for a given threshold, alpha, sample size N and number of allele frequencies. Choose FALSE if you already ran powerCurves() outside or do not want to show power curves.`show_power_curves`

: (TRUE/FALSE) Show power curves in plot. Needs argument`calculate_power = TRUE`

.`threshold`

: (Required if calculate_power == TRUE). Can be a single number or a vector of statistical power thresholds.`N`

: (Required if calculate_power == TRUE). Sample size used to test the association.`alpha`

: (Required if calculate_power == TRUE).

`Nfreq`

: (Required if calculate_power == TRUE). Number of allele frequency data points generated to calculate the power curves. We recommend Nfreq>1000 for power curves with high resolution. Note that this will slow down the rendering of the plot.`power_color_palette`

: A vector of colours for the power curves. Number of colors should match number of thresholds supplied.`analysis_color_palette`

: A vector of colours for the argument`Analysis`

.`trait`

: (optional) Name of the trait.

A ‘toy_data’ dataset is provided to test the function. This toy_data contains 8000 genetic associations and seven columns to showcase function ‘trumpets’. Data was obtained from GWAS and exome sequencing association analyses performend in the UK Biobank.

- Load the toy dataset:
`data(toy_data)`

- Run the trumpets function:
`plot_trumpets(dataset = toy_data)`

For users with no knowledge of R, and to visualize Trumpet plots for >100 traits in the UK Biobank, visit the R Shiny application “Shiny Trumpets”, available at: https://juditgg.shinyapps.io/shinytrumpets/

For questions/issues related to the R package, visit https://gitlab.com/JuditGG/trumpetplots/-/issues

For questions/issues related to the R Shiny app, visit https://gitlab.com/JuditGG/freq_or_plots/-/issues