# Grab the WD from the file location and set it
library(rstudioapi)
home <- getActiveDocumentContext()$path
setwd(dirname(home)); getwd(); setwd('..')
home <- getwd(); getwd()
# Set my_theme for use with ggplot2
my_theme <- theme(line = element_line(size=1.5),
rect = element_rect(size=1.5),
text = element_text(size=14,color="black"),
panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.text.x = element_text(size=16,color="black"),
axis.text.y = element_text(size=16,color="black"),
axis.title.x = element_text(margin = margin(t = 10, r = 0, b = 0, l = 0)),
axis.title.y = element_text(margin = margin(t = 0, r = 10, b = 0, l = 0)),
axis.ticks.x = element_line(color="black"),
axis.ticks.y = element_line(color="black"),
# axis.line = element_line(color = "black", size = 0.1),
panel.border = element_rect(color = "black", fill=NA, size=1.5),
legend.key = element_blank()) # removes background of legend bullets
# Add all required libraries that are installed with install.packages() here
list.of.packages <- c("tidyverse", "lubridate")
# Add all libraries that are installed using BiocManager here
bioconductor.packages <- c("DESeq2", "WGCNA")
# Install BiocManager if needed
if(!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
# Get names of all required packages that aren't installed
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[, "Package"])]
new.bioc.packages <- bioconductor.packages[!(bioconductor.packages %in% installed.packages()[, "Package"])]
# Install all new packages
if(length(new.packages)) install.packages(new.packages)
if(length(new.bioc.packages)) BiocManager::install(new.bioc.packages)
# Load all required libraries
all.packages <- c(list.of.packages, bioconductor.packages)
lapply(all.packages, FUN = function(X) {
do.call("require", list(X))
})