HGG-oncohistones project [source]
04 - Analysis of thalamic H3K27M tumors
Selin Jessa []
12 September, 2022
1 Configuration
Configuration of project directory & analysis outputs:
Show full config
source(here("rr_helpers.R"))
# Set up outputs
message("Document index: ", doc_id)## Document index: 04# Specify where to save outputs
out <- here("output", doc_id); dir.create(out, recursive = TRUE)
figout <- here("figures", doc_id); dir.create(figout, recursive = TRUE)
cache <- paste0(readLines(here("include/project_root.txt")), basename(here()), "/", doc_id, "/")Outputs and figures will be saved at these paths, relative to project root:
## public/output/04## public/figures/04Setting a random seed:
set.seed(100)2 Overview
In this document, we investigate the activation of diencephalon patterning genes in thalamic gliomas as shown in Figure 3.
3 Libraries
# Load libraries here
library(here)
library(tidyr)
library(dplyr)
library(GenomicRanges)
library(BentoBox)
library(BSgenome.Hsapiens.UCSC.hg19)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
library(rtracklayer)
library(ggrepel)
library(readr)
library(glue)
library(tibble)
library(ggplot2)
library(purrr)
library(cowplot)
source(here("include/style.R"))
source(here("code/functions/BentoBox_helpers.R"))
source(here("code/functions/RNAseq.R"))
source(here("code/functions/scRNAseq.R"))
ggplot2::theme_set(theme_min())4 Load metadata
Load the sample metadata for the project:
meta <- read_tsv(here("data/metadata/metadata_patient_samples_NGS.tsv"))meta_chip <- read_tsv(here("data/metadata/metadata_chip_all.tsv")) %>%
right_join(meta, by = c("BioID", "ID_paper", "Material")) %>%
mutate(Factor = gsub("-M", "", Factor)) %>%
filter(grepl("Cell-of-origin", Analyses))5 Activation of prosomere markers
To map thalamic tumors to the prosomeres of the diencephalon, we'll assess the activation of various prosomere 2/3 markers in the tumors based on RNAseq, H3K27ac and H3K27me3:
# set genes to examine
prosomere_markers <- list(
GRanges("chr3", 147093346:147150046, name = "ZIC1/4"),
GRanges("chr2", 63273543:63289360, name = "OTX1"),
GRanges("chr2", 237071880:237079029, name = "GBX2"),
GRanges("chr16", 54315217:54322699, name = "IRX3"),
GRanges("chr7", 2544962:2574432, name = "LFNG"),
GRanges("chr10", 119295203:119315811, name = "EMX2"),
GRanges("chr2", 45163986:45175965, name = "SIX3"),
GRanges("chr7", 121940057:121946104, name = "FEZF1"))
# make params
params_prosomere <- map(prosomere_markers, ~ bb_params(chrom = as.character(seqnames(.x)),
chromstart = start(.x),
chromend = end(.x),
assembly = "hg19"))
names(params_prosomere) <- map(prosomere_markers, ~ .x$name)# load in track configuration
prosomere_config <- prep_track_input(here("data/BentoBox_config/prosomere_thalamus.config.tsv"))Make a summary figure of the tracks at these regions. In pseudocode:
for each region:
-- for each sample:
----- plot signal & annotation
----- plot genome label
Generate figure:
x_positions <- seq(0.5, 15, by = 1.75)
y_positions <- seq(0.5, by = 0.4, length.out = nrow(prosomere_config))
bb_pageCreate(width = 15, height = 7, default.units = "inches")
for (i in seq_along(params_prosomere)) {
x_i <- x_positions[i]
params_i <- params_prosomere[[i]]
# iterating through samples,
# plot H3K27ac and H3K27me3
pwalk(list(prosomere_config$bw, prosomere_config$ID_paper, prosomere_config$Data, prosomere_config$Ymax, y_positions),
~ bb_placeSignalAndLabel(data = ..1,
annotation = ..2,
color = palette_tracks[..3],
range = c(0, ..4),
y = ..5, x = x_i,
params = params_i,
width = 1.5,
height = 0.35,
fontsize = 4))
# place 0.03in below last plot
bb_plotGenomeLabel(params = params_i, scale = "Kb", x = x_i, y = "0.03b", length = 1.5, fontsize = 8)
bb_plotGenes(params = params_i, x = x_i, y = "0.05b", height = 1.5, width = 1.5,
strandcolors = c("navy", "black"), fontcolors = c("navy", "black"),
stroke = 0.05,
just = c("left", "top"), default.units = "inches")
}
bb_pageGuideHide()
6 Reproducibility
This document was last rendered on:
## 2022-09-12 15:22:30The git repository and last commit:
## Local: master /lustre06/project/6004736/sjessa/from_narval/HGG-oncohistones/public
## Remote: master @ origin (git@github.com:fungenomics/HGG-oncohistones.git)
## Head: [1a06382] 2022-09-08: Update comments, documentation, etc, based on lab feedbackThe random seed was set with set.seed(100)
The R session info:
## Error in get(genname, envir = envir) : object 'testthat_print' not found## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.1 (2019-07-05)
## os Rocky Linux 8.6 (Green Obsidian)
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_CA.UTF-8
## ctype en_CA.UTF-8
## tz EST5EDT
## date 2022-09-12
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date lib
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## source
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## Github (PhanstielLab/BentoBox@72701d1)
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## Github (rmflight/testrmd@0735c20)
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