mirror of
https://github.com/johrpan/ubigen.git
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139 lines
3.2 KiB
R
139 lines
3.2 KiB
R
library(data.table)
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library(here)
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i_am("scripts/comparison.R")
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w2000 <- scan(here("scripts/input/datasets/warrington_2000.txt"), character())
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z2008 <- scan(here("scripts/input/datasets/zhu_2008.txt"), character())
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e2013 <- scan(here("scripts/input/datasets/eisenberg_2013.txt"), character())
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c2011 <- scan(here("scripts/input/datasets/chang_2011.txt"), character())
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j2022 <- scan(here("scripts/input/datasets/joshi_2022.txt"), character())
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datasets <- list(
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"Warrington 2000" = w2000,
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"Zhu 2008" = z2008,
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"Eisenberg 2013" = e2013,
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"Chang 2011" = c2011,
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"Joshi 2022" = j2022
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)
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VennDiagram::venn.diagram(datasets, filename = NULL, disable.logging = TRUE) |>
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ggplot2::ggsave(file = here("scripts/output/venn.svg"), device = "svg")
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partitions <- VennDiagram::get.venn.partitions(datasets) |> data.table()
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genes_venn <- partitions[1]$..values..[[1]]
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write(genes_venn, file = here("scripts/output/genes_venn.txt"))
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ranking_gtex <- ubigen::rank_genes(ubigen::gtex_all)
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ranking_cmap <- ubigen::rank_genes(ubigen::cmap)
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data <- merge(
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ranking_gtex[, .(gene, score, percentile)],
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ranking_cmap[, .(gene, score, percentile)],
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by = "gene",
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suffixes = c(x = "_gtex", y = "_cmap")
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)
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data[, count := 0]
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for (dataset in datasets) {
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data[gene %chin% dataset, count := count + 1]
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}
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threshold_gtex <- data[percentile_gtex >= 0.95, min(score_gtex)]
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threshold_cmap <- data[percentile_cmap >= 0.95, min(score_cmap)]
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fig <- plotly::plot_ly() |>
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plotly::add_markers(
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data = data,
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x = ~score_gtex,
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y = ~score_cmap,
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color = ~count,
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colors = c("#7d19bf", "#ff7f2a"),
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marker = list(
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size = 4,
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opacity = 0.8
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),
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cliponaxis = FALSE
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) |>
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plotly::layout(
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xaxis = list(
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title = "Ranking based on GTEx",
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range = c(0, 1)
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),
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yaxis = list(
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title = "Ranking based on CMap",
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range = c(0, 1)
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),
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annotations = list(
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list(
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text = "95%",
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x = threshold_gtex,
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y = 1,
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xshift = 2,
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yshift = 3,
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yref = "paper",
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xanchor = "left",
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yanchor = "top",
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showarrow = FALSE
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),
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list(
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text = "95%",
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x = 1,
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y = threshold_cmap,
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yshift = 2,
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xref = "paper",
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xanchor = "right",
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yanchor = "bottom",
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showarrow = FALSE
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)
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),
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shapes = list(
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list(
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type = "line",
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y0 = 0,
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y1 = 1,
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yref = "paper",
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x0 = threshold_gtex,
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x1 = threshold_gtex,
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line = list(
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color = "#00000080",
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opacity = 0.5,
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width = 1,
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dash = "dot"
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)
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),
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list(
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type = "line",
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y0 = threshold_cmap,
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y1 = threshold_cmap,
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x0 = 0,
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x1 = 1,
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xref = "paper",
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line = list(
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color = "#00000080",
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width = 1,
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opacity = 0.5,
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dash = "dot"
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)
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)
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),
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font = list(size = 8),
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margin = list(
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pad = 2,
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l = 36,
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r = 0,
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t = 0,
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b = 36
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)
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) |>
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plotly::hide_legend() |>
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plotly::hide_colorbar()
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plotly::save_image(
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fig,
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file = here("scripts/output/comparison.svg"),
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width = 6.27 * 72,
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height = 6.27 * 72,
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scale = 96 / 72
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)
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