From 4fd2fbf31b45abce4257a8b904c72380a73dd7d7 Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Thu, 25 Jul 2024 22:12:22 +0200
Subject: [PATCH] fix: remove unneeded qmd vignette

---
 vignettes/manuscript_figure.qmd | 130 --------------------------------
 1 file changed, 130 deletions(-)
 delete mode 100644 vignettes/manuscript_figure.qmd

diff --git a/vignettes/manuscript_figure.qmd b/vignettes/manuscript_figure.qmd
deleted file mode 100644
index c53a986..0000000
--- a/vignettes/manuscript_figure.qmd
+++ /dev/null
@@ -1,130 +0,0 @@
----
-title: "Figure for tidyCoverage manuscript"
----
-
-```{r setup, include = FALSE}
-knitr::opts_chunk$set(
-    collapse = TRUE,
-    comment = "#>",
-    crop = NULL, 
-    width = 180, 
-    error = TRUE
-)
-```
-
-# Plotting aggregate signals (ENCODE data) over REs
-
-```{r}
-library(tidyCoverage)
-library(AnnotationHub)
-library(purrr)
-library(plyranges)
-library(rtracklayer)
-library(ggplot2) 
-
-# ~~~~~~~~~~ Tracks ~~~~~~~~~~ #
-ids <- c(
-    fwdGRO = "ENCFF896TNM", 
-    revGRO = "ENCFF764SVR", 
-    Pol2RA = "ENCFF890SYC", 
-    CTCF = "ENCFF484SOD", 
-    DNAse = "ENCFF428XFI", 
-    ATAC = "ENCFF165WGA", 
-    H3K4me1 = "ENCFF785YET", 
-    H3K4me3 = "ENCFF736DCK", 
-    H3K9me3 = "ENCFF698SKV", 
-    H3K27me3 = "ENCFF119CAV", 
-    H3K27ac = "ENCFF458CRP"  
-)
-future::plan(future::multisession(workers = 13))
-options(timeout=10000)
-furrr::future_map(ids[7:13], ~ {
-    download.file(glue::glue("https://www.encodeproject.org/files/{.x}/@@download/{.x}.bigWig"), glue::glue("encode/{.x}.bigWig"))
-})
-tracks <- rtracklayer::BigWigFileList(paste0('encode/', ids, '.bigWig'))
-names(tracks) <- names(ids)
-
-# ~~~~~~~~~~ REs ~~~~~~~~~~ #
-download.file('https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-020-2493-4/MediaObjects/41586_2020_2493_MOESM12_ESM.txt', 'data/REs_GRCh38.txt')
-features <- vroom::vroom('data/REs_GRCh38.txt', col_names = TRUE, show_col_types = FALSE) |> 
-    filter(chr == 'chr1') |> 
-    filter(group %in% c('PLS,CTCF-bound', 'pELS,CTCF-bound', 'pELS', 'dELS,CTCF-bound', 'dELS')) |>
-    group_by(group) |> 
-    dplyr::slice_head(n = 10000) |> 
-    makeGRangesFromDataFrame(keep.extra.columns = TRUE)
-genome(features) <- 'hg38'
-REs <- split(features, features$group)
-
-# ~~~~~~~~~~ Computing coverage of all tracks over all features ~~~~~~~~~~ #
-library(BiocParallel)
-register(MulticoreParam(workers = 13, progressbar = TRUE))
-CE <- CoverageExperiment(
-    tracks = tracks, 
-    features = REs, 
-    width = 5000, 
-    window = 5
-) 
-AC <- aggregate(CE)
-
-# ~~~~~~~~~~ Plot the resulting AggregatedCoverage object ~~~~~~~~~~ #
-AC |> 
-    as_tibble() |> 
-    group_by(track, features) |> 
-    mutate(group = dplyr::case_when(
-        stringr::str_detect(track, 'RNA|GRO') ~ "RNA", 
-        stringr::str_detect(track, 'CTCF|DNAse|ATAC') ~ "Accessibility", 
-        stringr::str_detect(track, 'H3') ~ "Histone PTMs"
-    )) |> 
-    # mutate(across(all_of(c("mean", "ci_low", "ci_high")), ~ ifelse(group == 'RNA', scale(.x), .x))) |> 
-    mutate(group = factor(group, c("RNA", "Accessibility", "Histone PTMs"))) |> 
-    mutate(track = factor(track, names(ids))) |> 
-    tidyr::drop_na() |> 
-    ggplot(aes(x = coord, y = mean)) + 
-    geom_ribbon(aes(ymin = ci_low, ymax = ci_high, fill = track), alpha = 0.2) + 
-    geom_line(aes(col = track)) + 
-    facet_grid(group~features, scales = 'free') + 
-    labs(x = 'Distance from center of reg. elements', y = 'Track signal') + 
-    theme_bw() + 
-    theme(legend.position = 'top') + 
-    hues::scale_colour_iwanthue() + 
-    hues::scale_fill_iwanthue() 
-```
-
-# Plotting matrix signals (ENCODE data) over REs
-
-```{r}
-expand(CE) |> 
-    filter(track == "ATAC") |> 
-    select(-coord) |> 
-    nest(data = c(coord.scaled, coverage)) |> 
-    mutate(score = map_dbl(
-        data, 
-        ~ filter(.x, abs(coord.scaled) < 50) |> pull(coverage) |> mean(na.rm = TRUE)
-    )) |> 
-    unnest(data) |>
-    arrange(score) |> 
-    mutate(coverage = scales::oob_squish(coverage, c(0, 10))) |> 
-    ggplot(aes(x = coord.scaled, y = factor(ranges, unique(ranges)), fill = coverage)) + 
-    geom_tile() |> ggrastr::rasterize() + 
-    facet_wrap(~ features, scales = 'free') + 
-    scale_fill_distiller(palette = 'Spectral', direction = -1) + 
-    scale_x_continuous(expand = c(0,0)) + 
-    theme_bw() + 
-    theme(
-        legend.position = 'bottom', 
-        axis.text.y = element_blank(), 
-        axis.ticks.y = element_blank()  
-    )
-
-as_tibble(AC) |> filter(track == "ATAC", features == 'PLS,CTCF-bound') |> 
-    pivot_longer(all_of(c("mean", "median", "ci_low", "ci_high")), names_to = 'coverage', values_to = 'score') |> 
-    ggplot(aes(x = coord, y = score, col = coverage)) + 
-        geom_path() +
-        facet_grid(~ coverage)
-```
-
-# Session info 
-
-```{r}
-sessioninfo::session_info()
-```