GENI plots

Overview

The geni.plots R package is a tool for visualising results from genome-wide association studies (GWAS) and phenome-wide association studies (PheWAS). The package can currently produce Manhattan plots, quantile-quantile (QQ) plots, and regional plots using GWAS summary statistics using the fig_manhattan(), fig_qq(), and fig_region() functions, respectively. In addition, PheWAS plots can be constructed using the fig_phewas() function.

library(dplyr)
library(geni.plots)

Functions

The package contains the following functions:

  • fig_manhattan: creates a Manhattan plot for genomic markers from across the genome, e.g. results from genome-wide association studies.
  • fig_phewas: creates a plot visualising results from phenome-wide association studies (PheWAS).
  • fig_qq: creates a quantile-quantile (QQ) plot.
  • fig_region: creates a regional plot, i.e. a scatter graph of genomic marker associations (e.g. log10(p-values)) with a gene bar underneath.
  • fig_stack_region: creates a stacked regional association plot.

Data

The package contains formatted test data downloaded from FinnGen r9 (1:154426970-A-C) and from GWAS studies on IL6 (GCST90274815) and IL6R (GCST90274815) levels from the GWAS Catalog server.

  • geni_test_manhattan- a data.frame of results from a GWAS of interleukin-6 levels with p-values < 1e-3 (GCST90274815). The genomic coordinates used are GRCh37. A description of this data can be viewed using help(geni_test_gwas).
  • geni_test_phewas- a data.frame of PheWAS results for rs from FinnGen r9 (1:154426970-A-C). A description of this data can be viewed using help(geni_test_phewas).
  • geni_test_region- a list containing:
    • assoc - a data.frame of results from a GWAS of interleukin-6 levels for the GRCh37 region 1:154301970-154551970 (GCST90274815). The genomic coordinates used are GRCh37. A description of this data can be viewed using help(geni_test_region).
    • corr - a matrix of correlation statistics for the markers in assoc using the European samples from 1000 Genomes Phase 3. The genomic coordinates used are GRCh37.
  • geni_test_stack_region- a list containing:
    • assoc - a data.frame of results from GWAS studies on interleukin-6 and interleukin 6 receptor levels for the GRCh37 region 1:154301970-154551970 (GCST90274815 and GCST90088597). The genomic coordinates used are GRCh37. A description of this data can be viewed using help(geni_test_region).
    • corr - a matrix of correlation statistics for the markers in assoc using the European samples from 1000 Genomes Phase 3. The genomic coordinates used are GRCh37.

Plots

Manhattan plot

geni.plots::geni_test_manhattan %>%
  as_tibble() %>%
  head()
#> # A tibble: 6 × 6
#>   chr       pos    pvalue highlight highlight_shape label
#>   <chr>   <int>     <dbl>     <dbl>           <dbl> <chr>
#> 1 1      963661 0.000154          0               0 ""   
#> 2 1      968251 0.000538          0               0 ""   
#> 3 1     1010040 0.000167          0               0 ""   
#> 4 1     1112698 0.000682          0               0 ""   
#> 5 1     2031103 0.0000897         0               0 ""   
#> 6 1     2036650 0.000207          0               0 ""
fig_manhattan(
  data = geni.plots::geni_test_manhattan,
  block_thresh = 1e-4,
  label_box = TRUE
)
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the geni.plots package.
#>   Please report the issue at <https://github.com/jrs95/geni.plots/issues>.
#> This warning is displayed once per session.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.

Further details regarding functionality of the fig_manhattan function can be viewed using the command help(fig_manhattan).

PheWAS plot

geni.plots::geni_test_phewas %>%
  as_tibble() %>%
  head()
#> # A tibble: 6 × 5
#>   pvalue  sign group                    label                              text 
#>    <dbl> <dbl> <chr>                    <chr>                              <chr>
#> 1 0.375     -1 AB1: Infectious diseases Actinomycosis                      Phen…
#> 2 0.0506     1 AB1: Infectious diseases Amoebiasis                         Phen…
#> 3 0.112      1 AB1: Infectious diseases Anogenital herpesviral [herpes si… Phen…
#> 4 0.287     -1 AB1: Infectious diseases Aspergillosis                      Phen…
#> 5 0.0352    -1 AB1: Infectious diseases Atypical virus infections of cent… Phen…
#> 6 0.0113     1 AB1: Infectious diseases Bacterial, viral and other infect… Phen…
fig_phewas(
  data = geni.plots::geni_test_phewas,
  axis_text_angle = -70,
  axis_text_size = 10,
  label_size = 3.5
)

Note: this figure can be made interactive by setting interactive = TRUE.

Further details regarding functionality of the fig_phewas function can be viewed using the command help(fig_phewas).

QQ plot

Simple

fig_qq(
  pvalues = geni.plots::geni_test_phewas$pvalue
)
#> Ignoring unknown labels:
#> • fill : "Group"

Further details regarding functionality of the fig_qq function can be viewed using the command help(fig_qq).

Categories

fig_qq(
  data = geni.plots::geni_test_phewas %>%
    select(pvalue, group, label, text),
  legend_title = "Category",
  legend_title_size = 10,
  legend_text_size = 8
)

Note: this figure can be made interactive by setting interactive = TRUE.

Further details regarding functionality of the fig_qq function can be viewed using the command help(fig_qq).

Regional plot

Regional plot

fig_region(
  data = geni.plots::geni_test_region$assoc,
  corr = geni.plots::geni_test_region$corr,
  build = 37
)

Note:

  1. this figure can be made interactive by setting interactive = TRUE
  2. corr has to have the same markers as assoc in the same order
  3. by default fig_region assumes corr (or corr_top) contains correlation statistics that have not been squared, if corr is a squared correlation matrix set r2 = TRUE

Further details regarding functionality of the fig_region function can be viewed using the command help(fig_region).

Stacked regional plot

fig_region_stack(
  data = geni.plots::geni_test_stack_region$assoc,
  traits = c("Interleukin-6 levels", "Interleukin-6 receptor levels"),
  corr = geni.plots::geni_test_stack_region$corr,
  build = 37,
  highlights = "rs11265611",
  title_center = TRUE
)

Note:

  1. this figure can be made interactive by setting interactive = TRUE
  2. corr has to have the same markers as assoc in the same order
  3. by default fig_region_stack assumes corr (or corr_top) contains correlation statistics that have not been squared, if corr is a squared correlation matrix set r2 = TRUE

Further details regarding functionality of the fig_region_stack function can be viewed using the command help(fig_region_stack).