ubigen/scripts/gsea.R

# This script performs a gene set enrichment analysis (GSEA) across the whole
# ranking of ubiquituos genes using g:Profiler.

# Size of each gene bucket. The GSEA is done once for each bucket within the
# ranking.
bucket_size <- 500

library(data.table)
library(here)

i_am("scripts/gsea.R")
file_path <- here("scripts", "output", "ubigen_gsea.Rds")
image_path <- here("scripts", "output", "ubigen_gsea.svg")

# The result will be saved in `file_path` to avoid unnecessary API calls.
result <- if (file.exists(file_path)) {
  readRDS(file_path)
} else {
  data <- copy(ubigen::genes)
  data[, bucket := ceiling(rank / bucket_size)]

  result <- data[, .(analysis = list(gprofiler2::gost(gene))), by = bucket]
  saveRDS(result, file = file_path)

  result
}

result[, result := lapply(analysis, function (a) a$result)]
result <- result[, rbindlist(result), by = bucket]

data <- result[, .(count = .N), by = c("bucket", "source")]

fig <- plotly::plot_ly() |>
  plotly::add_bars(
    data = data,
    x = ~bucket,
    y = ~count,
    color = ~source
  ) |>
  plotly::layout(
    xaxis = list(title = "Bucket of genes (n = 500)"),
    yaxis = list(title = "Number of associated terms"),
    barmode = "stack",
    legend = list(title = list(text = "<b>Source of term</b>"))
  )

plotly::save_image(fig, image_path, width = 1200, height = 800)

gsea_plot_ranking <- fig
usethis::use_data(gsea_plot_ranking, internal = TRUE, overwrite = TRUE)