adamsardar

#%%

import copy
import timeit
import pandas as pd
import polars as pl

#%%

# Use pandas, but no need to make a defensive copy

adamsardar

pkgDeps <- remotes::local_package_deps('.', dependencies=TRUE);

pkgDeps <- setdiff(pkgDeps, .packages(all.available = TRUE));

debCRANpkgs <- tolower(paste('r-cran-', pkgDeps, sep = ''));
debBIOCpkgs <- tolower(paste('r-bioc-', pkgDeps, sep = ''));

debPkgsAvailable <- RcppAPT::hasPackages(c(debCRANpkgs,debBIOCpkgs));
binariesToInstall <- names(debPkgsAvailable)[which(debPkgsAvailable)];

adamsardar

#Set command prefix to be like screen
set -g prefix C-a
unbind C-b
bind C-a send-prefix

#Set up the status bar
set -g status-right '#[fg=green][#[fg=blue]%Y-%m-%d #[fg=yellow]%H:%M#[default]#[fg=green]]'
set -g status-bg black
set -g status-fg white
set -g status-left '#[fg=green]#(echo `whoami`)#[fg=white]@#[fg=magenta]#H'

adamsardar

#Including arch is useful for times that one might be running two versions of R on different architectures. e.g. on new M1 Macs
libDirectory <- paste(c("~/Rlibs/", R.Version()$minor, "/", R.Version()$arch, "/"),collapse="")
.libPaths(libDirectory)

#Taken from bioconductor. This removes the need for using biocLite to install packages, which would be at the top of my list of "Bad Things About R"
biocVersion <- "3.12"

biocMirror <- getOption("BioC_mirror", "https://bioconductor.org")
biocPaths <- c(BioCsoft = "bioc", BioCann = "data/annotation", BioCexp = "data/experiment")

adamsardar

pacman::p_load(igraph,stringr,data.table,utils,ensurer,magrittr)

#' Write an igraph object to file in graphML format
#' 
#' A frustrating feature of igraph is the lack of ability to affect the nodeID field of an output graphML file.
#' I ended up becoming so frustrated that I just wrote my own.
#' 
#' @param graph2Write An igraph object containing a uniquely labelled 'name' vertex attribute (which is used as nodeID)
#' @param filename The filename to write out the graphml file to
#' @return filename The filename of the graphML file

adamsardar

pacman::p_load(igraph,data.table,magrittr)


mergeGraphs <- function(...,desiredEdgeAttributes = c("from","to","edge_type"), omitNAnodes = TRUE){

  graphList <- list(...)
  
  tryCatch({