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119 lines
2.6 KiB
R
119 lines
2.6 KiB
R
library(data.table)
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library(here)
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i_am("scripts/datasets.R")
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ranking_gtex_all <- ubigen::rank_genes(ubigen::gtex_all)
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ranking_gtex_tissues <- ubigen::rank_genes(ubigen::gtex_tissues)
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ranking_hpa <- ubigen::rank_genes(ubigen::hpa_tissues)
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ranking_cmap <- ubigen::rank_genes(ubigen::cmap)
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cor_ranking <- function(ranking_x, ranking_y) {
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data <- merge(ranking_x, ranking_y, by = "gene")
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stats::cor(
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data$score.x,
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data$score.y,
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) |>
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round(digits = 4) |>
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format(nsmall = 4)
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}
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cat("Ranking correlations:")
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cat("\nGTEx (tissues) ~ GTEx (all): ")
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cat(cor_ranking(ranking_gtex_all, ranking_gtex_tissues))
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cat("\nHPA ~ GTEx (all): ")
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cat(cor_ranking(ranking_gtex_all, ranking_hpa))
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cat("\nCMap ~ GTEx (all): ")
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cat(cor_ranking(ranking_gtex_all, ranking_cmap))
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cat("\nCMap ~ GTEx (tissues): ")
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cat(cor_ranking(ranking_gtex_tissues, ranking_cmap))
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cat("\nHPA ~ GTEx (tissues): ")
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cat(cor_ranking(ranking_gtex_tissues, ranking_hpa))
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cat("\nCMap ~ HPA: ")
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cat(cor_ranking(ranking_hpa, ranking_cmap))
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# Sample rankings for plots
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sample_ranking <- function(ranking) {
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ranking <- ranking[percentile >= 0.8]
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ranking[sample(nrow(ranking), 500)]
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}
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fig <- plotly::plot_ly() |>
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plotly::add_lines(
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data = ranking_gtex_tissues |> sample_ranking(),
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x = ~percentile,
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y = ~score,
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name = "GTEx (tissues)",
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line = list(
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color = "#2275d4",
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width = 4
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)
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) |>
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plotly::add_lines(
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data = ranking_hpa |> sample_ranking(),
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x = ~percentile,
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y = ~score,
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name = "HPA (tissues)",
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line = list(
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color = "#30c422",
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width = 4
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)
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) |>
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plotly::add_lines(
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data = ranking_cmap |> sample_ranking(),
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x = ~percentile,
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y = ~score,
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name = "CMap (drugs)",
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line = list(
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color = "#ff7f2a",
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width = 4
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)
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) |>
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plotly::add_lines(
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data = ranking_gtex_all |> sample_ranking(),
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x = ~percentile,
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y = ~score,
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name = "GTEx (all)",
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line = list(
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color = "#7d19bf",
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width = 4
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)
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) |>
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plotly::layout(
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xaxis = list(
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title = "Percentile",
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tickformat = ".1%",
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range = c(0.8, 1)
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),
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yaxis = list(
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title = "Score",
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range = c(0, 1)
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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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showlegend = FALSE
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)
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plotly::save_image(
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fig,
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file = here("scripts/output/datasets.svg"),
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width = 6.27 * 72,
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height = 3.135 * 72,
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scale = 96 / 72
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)
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plotly::save_image(
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fig |> plotly::layout(showlegend = TRUE),
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file = here("scripts/output/datasets_legend.svg"),
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width = 6.27 * 72,
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height = 3.135 * 72,
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scale = 96 / 72
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)
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