Mehrad Mahmoudian mmahmoudian

How to use Neovim or VIM Editor as an IDE for R

Note: This tutorial is written for Linux based systems.

Requirements

R >= 3.0.0

To install the latest version of R please flollow the download and install instructions at https://cloud.r-project.org/

Neovim >= 0.2.0

Neovim (nvim) is the continuation and extension of Vim editor with the aim to keep the good parts of Vim and add more features. In this tutorial I will be using Neovim (nvim), however, most of the steps are equally applicable to Vim also. Please follow download and installation instructions on nvim's GitHub wiki https://github.com/neovim/neovim/wiki/Installing-Neovim.

Arch Linux tweaks

This is a collection of the tweaks and modification I've made to my Arch Linux installation over the months. These may be applicable to other distros, but please check first before doing anything. I also included Arch Wiki references for all the procedures I mentioned. My recommendation is not to blindly follow this gist but to always check with the Arch Linux wiki first. Things move fast and by the time you're reading this my gist may be out of date. Lastly, the golden rule: never execute a command you don't understand.

Installing the KDE Plasma desktop

My current DE of choice is KDE's Plasma. I find it just about perfect.

There are various ways to install it on Arch. The most popular one is to install plasma and plasma-applications, but I don't like doing that because it comes with too many programs I'll never use. I, instead, install the base plasma group, remove the few extra packages that come with it, then I finish off by installing a few KDE apps that don't come with th

Recovering deleted files in Ubuntu with ext4 filesystem

Recently, I deleted some files by mistake in a Ubuntu machine with an ext4 fs. These notes document the steps I took to get them back.

Important

this procedure assumes that the partition that contained the deleted files is different from the root partition, as that was the scenario with which I had to deal (deleted files were in my home dir). The procedure needs that the partition that contained the files is unmounted, so if the deleted files were in the root partition, the process would be a bit different (e.g. storing the fs journal in a USB stick, using a live CD/USB to boot and issue the commands, etc.)
if something is not clear, you need more information, etc. check the sources below

With that out the way, let's begin.

Disabling GNOME Tracker and Other Info

GNOME's tracker is a CPU and privacy hog. There's a pretty good case as to why it's neither useful nor necessary here: http://lduros.net/posts/tracker-sucks-thanks-tracker/

After discovering it chowing 2 cores, I decided to go about disabling it.

Directories

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname

	echo -e "\nHidden=true\n"\|sudo tee --append /etc/xdg/autostart/tracker-extract.desktop
	echo -e "\nHidden=true\n"\|sudo tee --append /etc/xdg/autostart/tracker-miner-apps.desktop
	echo -e "\nHidden=true\n"\|sudo tee --append /etc/xdg/autostart/tracker-miner-fs.desktop
	echo -e "\nHidden=true\n"\|sudo tee --append /etc/xdg/autostart/tracker-miner-user-guides.desktop
	echo -e "\nHidden=true\n"\|sudo tee --append /etc/xdg/autostart/tracker-store.desktop

	gsettings set org.freedesktop.Tracker.Miner.Files crawling-interval -2
	gsettings set org.freedesktop.Tracker.Miner.Files enable-monitors false

	tracker reset --hard

	#https://github.com/ateucher/useful_code/blob/master/R/numbers2words.r
	numbers2words <- function(x){
	## Function by John Fox found here:
	## http://tolstoy.newcastle.edu.au/R/help/05/04/2715.html
	## Tweaks by AJH to add commas and "and"
	helper <- function(x){

	digits <- rev(strsplit(as.character(x), "")[[1]])
	nDigits <- length(digits)
	if (nDigits == 1) as.vector(ones[digits])

	vioplot2 <- function (x, ..., range = 1.5, h = NULL, ylim = NULL, names = NULL,
	horizontal = FALSE, col = "magenta", border = "black", lty = 1,
	lwd = 1, rectCol = "black", colMed = "white", pchMed = 19,
	at, add = FALSE, wex = 1, drawRect = TRUE, side="both")
	{
	datas <- list(x, ...)
	n <- length(datas)
	if (missing(at))
	at <- 1:n
	upper <- vector(mode = "numeric", length = n)