ubigen/scripts/comparison.R

library(data.table)
library(here)

i_am("scripts/comparison.R")

w2000 <- scan(here("scripts/input/datasets/warrington_2000.txt"), character())
z2008 <- scan(here("scripts/input/datasets/zhu_2008.txt"), character())
e2013 <- scan(here("scripts/input/datasets/eisenberg_2013.txt"), character())
c2011 <- scan(here("scripts/input/datasets/chang_2011.txt"), character())
j2022 <- scan(here("scripts/input/datasets/joshi_2022.txt"), character())

datasets <- list(
  "Warrington 2000" = w2000,
  "Zhu 2008" = z2008,
  "Eisenberg 2013" = e2013,
  "Chang 2011" = c2011,
  "Joshi 2022" = j2022
)

VennDiagram::venn.diagram(datasets, filename = NULL, disable.logging = TRUE) |>
  ggplot2::ggsave(file = here("scripts/output/venn.svg"), device = "svg")

partitions <- VennDiagram::get.venn.partitions(datasets) |> data.table()
genes_venn <- partitions[1]$..values..[[1]]
write(genes_venn, file = here("scripts/output/genes_venn.txt"))

ranking_gtex <- ubigen::rank_genes(ubigen::gtex_all)
ranking_cmap <- ubigen::rank_genes(ubigen::cmap)

data <- merge(
  ranking_gtex[, .(gene, score, percentile)],
  ranking_cmap[, .(gene, score, percentile)],
  by = "gene",
  suffixes = c(x = "_gtex", y = "_cmap")
)

data[, count := 0]

for (dataset in datasets) {
  data[gene %chin% dataset, count := count + 1]
}

threshold_gtex <- data[percentile_gtex >= 0.95, min(score_gtex)]
threshold_cmap <- data[percentile_cmap >= 0.95, min(score_cmap)]

fig <- plotly::plot_ly() |>
  plotly::add_markers(
    data = data,
    x = ~score_gtex,
    y = ~score_cmap,
    color = ~count,
    colors = c("#7d19bf", "#ff7f2a"),
    marker = list(
      size = 4,
      opacity = 0.8
    ),
    cliponaxis = FALSE
  ) |>
  plotly::layout(
    xaxis = list(
      title = "Ranking based on GTEx",
      range = c(0, 1)
    ),
    yaxis = list(
      title = "Ranking based on CMap",
      range = c(0, 1)
    ),
    annotations = list(
      list(
        text = "95%",
        x = threshold_gtex,
        y = 1,
        xshift = 2,
        yshift = 3,
        yref = "paper",
        xanchor = "left",
        yanchor = "top",
        showarrow = FALSE
      ),
      list(
        text = "95%",
        x = 1,
        y = threshold_cmap,
        yshift = 2,
        xref = "paper",
        xanchor = "right",
        yanchor = "bottom",
        showarrow = FALSE
      )
    ),
    shapes = list(
      list(
        type = "line",
        y0 = 0,
        y1 = 1,
        yref = "paper",
        x0 = threshold_gtex,
        x1 = threshold_gtex,
        line = list(
          color = "#00000080",
          opacity = 0.5,
          width = 1,
          dash = "dot"
        )
      ),
      list(
        type = "line",
        y0 = threshold_cmap,
        y1 = threshold_cmap,
        x0 = 0,
        x1 = 1,
        xref = "paper",
        line = list(
          color = "#00000080",
          width = 1,
          opacity = 0.5,
          dash = "dot"
        )
      )
    ),
    font = list(size = 8),
    margin = list(
      pad = 2,
      l = 36,
      r = 0,
      t = 0,
      b = 36
    )
  ) |>
  plotly::hide_legend() |>
  plotly::hide_colorbar()

plotly::save_image(
  fig,
  file = here("scripts/output/comparison.svg"),
  width = 6.27 * 72,
  height = 6.27 * 72,
  scale = 96 / 72
)