| Title: | Visualising Variant Set Association Test Results |
| Version: | 0.1.0 |
| License: | MIT + file LICENSE |
| Language: | en-GB |
| Description: | Provides a graphical method for joint visualisation of Variant Set Association Test (VSAT) results and individual variant association statistics. The Archipelago method assigns genomic coordinates to variant set statistics, allowing simultaneous display of variant-level and set-level signals in a unified plot. This supports interpretation of both collective and individual variant contributions in genetic association studies using variant aggregation approaches. For more see Lawless et al. (2026) <doi:10.1002/gepi.70025>. |
| Encoding: | UTF-8 |
| Imports: | ggplot2, dplyr |
| RoxygenNote: | 7.3.3 |
| VignetteBuilder: | knitr |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| Depends: | R (≥ 4.1.0) |
| LazyData: | true |
| NeedsCompilation: | no |
| Packaged: | 2026-02-07 16:48:28 UTC; akira |
| Author: | Dylan Lawless 
[aut, cre, cph] |
| Maintainer: | Dylan Lawless <admin@switzerlandomics.ch> |
| Repository: | CRAN |
| Date/Publication: | 2026-02-10 21:00:02 UTC |
Archipelago Plot
Description
Plot p-values from variant and variant-set tests.
Arguments
df1 |
A dataframe of variant-set data. |
df2 |
A dataframe of variant data. |
plot_title |
Title for the plot. |
add_title |
Logical; add title if TRUE. |
plot_subtitle |
Subtitle for the plot. |
add_subtitle |
Logical; add subtitle if TRUE. |
chr_ticks |
Logical; show chromosome ticks if TRUE. |
show_legend |
Logical; display the legend if TRUE. |
color_theme |
Name of the colour theme. |
custom_colors |
Vector of custom colours. |
color_labels |
Labels for the colour groups. |
crit_val |
Critical p-value threshold. |
point_size |
Size of the points. |
point_size_large |
Size of the large points of interest such as VSAT. |
fig_width |
Width of the archipelago plot. |
fig_height |
Height of the archipelago plot. |
raw_fig_width |
Width of the raw plot. |
raw_fig_height |
Height of the raw plot. |
output_path |
File path for the plot. |
output_raw |
File path for the raw plot. |
file_type |
Use .png, .jpg, or .pdf. Defaults to png. pdf is slow and large for many SNPs. |
alpha_point |
Use the alpha_point value to set point transparency. |
alpha_seg |
Use the alpha_segvalue to set line segment transparency. |
better_space |
Use better_space = TRUE to make sure that x-axis chr do not squash. |
legend_position |
Default right, allows bottom top left right. |
annotate_thresholds |
Logical; if TRUE, annotate plot with VSAT and single-variant p-value thresholds. |
Value
A ggplot object.
Examples
data("vsat_pval")
data("variant_pval")
archipelago_plot(vsat_pval, variant_pval)
Example variant data
Description
Example variant-level p-values from a genome-wide association study.
Usage
variant_pval
Format
A data frame with columns:
set_ID
BP
P
CHR
SNP
Example variant set data
Description
Example variant set-level p-values.
Usage
vsat_pval
Format
A data frame with columns:
set_ID
P