inst/scripts/lz.R

In gaawr2: Genetic Association Analysis

use_locuszoomr <- function()
{
  require(locuszoomr)
  require(EnsDb.Hsapiens.v75)

  data(SLE_gwas_sub,package="locuszoomr")
  head(SLE_gwas_sub)
  loc <- locuszoomr::locus(data = SLE_gwas_sub, gene = 'UBE2L3', flank = 1e5,
                           ens_db = "EnsDb.Hsapiens.v75")
  loc <- locuszoomr::link_LD(loc, token = Sys.getenv("LDLINK_TOKEN"))
  summary(loc)
  locuszoomr::locus_plot(loc)
  locuszoomr::locus_plot(loc, filter_gene_biotype = "protein_coding")
  locuszoomr::locus_plot(loc, filter_gene_name = c('UBE2L3', 'RIMBP3C', 'YDJC', 'PPIL2',
                                                   'PI4KAP2', 'MIR301B'))
  loc2 <- locuszoomr::locus(SLE_gwas_sub, gene = 'IRF5', flank = c(7e4, 2e5), LD = "r2",
                            ens_db = "EnsDb.Hsapiens.v75")
  require(rtracklayer)
  bw38 <- "https://hgdownload.soe.ucsc.edu/gbdb/hg38/recombRate/recomb1000GAvg.bw"
  bw19 <- "https://hgdownload.soe.ucsc.edu/gbdb/hg19/decode/hapMapRelease24CombinedRecombMap.bw"
  download.file(bw19, destfile = basename(bw19))
  recomb.hg19 <- rtracklayer::import.bw(basename(bw19))
  unlink(basename(bw19))
  loc3 <- locuszoomr::locus(SLE_gwas_sub, gene = 'STAT4', flank = 1e5, LD = "r2",
                            ens_db = "EnsDb.Hsapiens.v75")
  loc3 <- locuszoomr::link_recomb(loc3, recomb = recomb.hg19)
  locuszoomr::locus_plot(loc3)

  p1 <- locuszoomr::locus_ggplot(loc, labels = "index", nudge_x = 0.03)
  p2 <- locuszoomr::locus_ggplot(loc2, legend_pos = NULL)

  library(cowplot)
  cowplot::plot_grid(p1, p2, ncol = 1)

  library(ggpubr)
  ggpubr::ggarrange(p1, p2, ncol = 1)

  library(gridExtra)
  gridExtra::grid.arrange(p1, p2, ncol = 1)

  locuszoomr::locus_ggplot(loc)
  locuszoomr::gg_scatter(loc)
  locuszoomr::gg_genetracks(loc)
  p <- locuszoomr::gg_scatter(loc)
  locuszoomr::gg_addgenes(p, loc)
  locuszoomr::locus_plotly(loc)

  locuszoomr::multi_layout(ncol = 3,
               plots = {
                 locuszoomr::locus_plot(loc, use_layout = FALSE, legend_pos = 'topleft')
                 locuszoomr::locus_plot(loc2, use_layout = FALSE, legend_pos = NULL)
                 locuszoomr::locus_plot(loc3, use_layout = FALSE, legend_pos = NULL, labels = "index")
               })
}