NB-FOXR2 project [source]
01 - Oncoprint
Selin Jessa [selin.jessa@mail.mcgill.ca] and Bhavyaa Chandarana [bhavyaa.chandarana@mail.mcgill.ca]
09 October, 2024
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: 01# Specify where to save outputs
out <- here("output", doc_id); dir.create(out, recursive = TRUE)
figout <- here("figures", doc_id, "/")
cache <- paste0("/project/kleinman/bhavyaa.chandarana/cache/NB-FOXR2/public/", doc_id, "/")The root directory of this project is:
## /project/kleinman/bhavyaa.chandarana/from_hydra/2023-05-NB-FOXR2/publicOutputs and figures will be saved at these paths, relative to project root:
## public/output/01## public/figures/01//Setting a random seed:
set.seed(100)2 Overview
Here we produce an oncoprint as an overview of the dataset. This code is adapted from Steven Hébert.
3 Libraries
knitr::opts_chunk$set(cache = FALSE)
library(here)
library(data.table)
library(magrittr)
library(tidyr)
library(dplyr)
library(readr)
library(glue)
library(ggplot2)
library(ComplexHeatmap)
source(here("include/style.R"))
source(here("code/functions/scRNAseq.R"))
ggplot2::theme_set(theme_min())4 Load metadata
meta <- read_tsv(here("output/00/oncoprint.tsv"))## Rows: 125 Columns: 13
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (13): Sample, ID, FOXR2_positive, Group, Source, Age, Sex, Location, RNA...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.data <- as.data.table(meta)
# Show counts per group
table(data$Group)##
## DIPG-H3K27M DIPG-H3K27M-FOXR2 EP-PFA ETMR
## 19 6 13 12
## HGG-H3.3G34R/V HGG-IDH MB-SHH MB-WNT
## 18 10 8 10
## NB-FOXR2
## 295 Set heatmap annotation
palette_location <- c("Cerebellum" = "goldenrod3",
"Hemispheric" = "navy",
"Pons" = "gold1",
"Posterior Fossa" = "orange",
"Thalamus" = "darkolivegreen4",
"Unknown" = "gray80")
palette_bulkRNAseq <- c("Y" = "black",
"N" = "gray80")
palette_scRNAseq <- c("Y" = "black",
"N" = "gray80")
palette_scMultiome <- c("Y" = "black",
"N" = "gray80")
palette_newSample <- c("Y" = "black",
"N" = "gray80")
palette_FOXR2positive <- c("Y" = "black",
"N" = "gray80")
palette_sex <- c("M" = "black",
"F" = "gray80",
"Unknown" = "gray50")
# Set the order of the samples
samples_order <- data$ID
# Add additional info (row) on the bottom of the oncoprint
bot_ann <- HeatmapAnnotation(
annotation_name_gp = gpar(fontsize = 10),
Group = data$Group,
Location = data$Location_broad,
FOXR2_positive = data$FOXR2_positive,
Sex = data$Sex,
New_sample = data$New_sample,
bulkRNAseq = data$RNAseq,
scRNAseq = data$scRNAseq,
`Age(year)` = anno_points(as.matrix(as.numeric(data$Age)), border = F, size = unit(1, "mm")),
col = list(Group = palette_groups,
Location = palette_location,
FOXR2_positive = palette_FOXR2positive,
Sex = palette_sex,
New_sample = palette_newSample,
bulkRNAseq = palette_bulkRNAseq,
scRNAseq = palette_scRNAseq),
na_col = "white",
gp = gpar(col = "white"))6 Create oncoprint
# plot just the heatmap annotation by including an empty 0-row heatmap
# following: https://github.com/jokergoo/ComplexHeatmap/issues/301#issuecomment-487481520
Heatmap(matrix(nc = 125, nr = 0),
bottom_annotation = bot_ann)
7 Reproducibility
This document was last rendered on:
## 2024-10-09 18:18:33The git repository and last commit:
## Local: main /project/kleinman/bhavyaa.chandarana/from_hydra/2023-05-NB-FOXR2/public
## Remote: main @ origin (https://github.com/fungenomics/NB-FOXR2.git)
## Head: [0e89693] 2024-09-12: Initial commitThe random seed was set with set.seed(100)
The R session info:
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.2 (2021-11-01)
## os Rocky Linux 8.7 (Green Obsidian)
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/Toronto
## date 2024-10-09
## pandoc 1.19.2.1 @ /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/ (via rmarkdown)
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## [1] /project/kleinman/bhavyaa.chandarana/from_hydra/2023-05-NB-FOXR2/public/renv/library/R-4.1/x86_64-pc-linux-gnu
## [2] /home/kleinman/bhavyaa.chandarana/.cache/R/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/145cef2c
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A project of the Kleinman Lab at McGill University, using the rr reproducible research template.