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.
data(toy_data)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