Selin Jessa sjessa

Computational biologist & post-doc at Stanford: interested in the brain, functional genomics, and open science.

sjessa / knit.sh

Created July 6, 2018 20:10

knit Rmd from commandline

	# save in .bashrc
	# usage: knit 01-analysis.Rmd

	function knit() {
	R --no-save -e "rmarkdown::render('""$1""', 'html_document')"
	}

sjessa / prompt.sh

Last active July 6, 2018 20:01

simple bash prompt

	# to add to ~/.bashrc
	# e.g. selinjessa @ iMacPro @ ~ # 22846.test $
	export PS1="\[\e[34m\]\u \[\e[m\]@ \[\e[31m\]\h \[\e[m\]@ \[\e[36m\]\W \[\e[m\]# ${STY} $ "

sjessa / tidyeval_filter.R

Last active July 6, 2018 20:09

Filter a data frame based on a set of expressions

	# Filters

	library(tidyverse)

	sample_filters <- quos(project %in% c("dev", species %in% c("mouse")))

	sample_list <- data.frame(
	project = c("dev", "pbt"),
	species = c("mouse", "human"),
	dont_filter = c("a", "b"))

sjessa / setup

Last active June 28, 2017 18:17

My preferred knitr chunk settings for R Markdown documents

	```{r setup, echo = FALSE, message = FALSE, warning = FALSE}

	knitr::opts_chunk$set(dev = "pdf", # Save figures as PDFs
	fig.keep = "all",
	fig.path = "figures/", # Figures are saved to this directory
	message = FALSE, # Hide messages/warnings/errors from loading packages
	warning = FALSE,
	error = FALSE,
	cache = TRUE) # By default, cache results to avoid re-running
	# super long things every time you knit

sjessa / knitsnapshot.sh

Created May 1, 2017 14:18

Knit an R Markdown document from the commandline, and specify the output filename

R -e 'library(knitr); knit("report.Rmd", "report.md")'; pandoc report.md --output snapshot.pdf --variable 'geometry:margin=1in'

sjessa / selinj.zsh-theme

Created September 27, 2016 16:36

My zsh theme

	PROMPT=" %{$fg[magenta]%}%n%{$reset_color%} @ %{$fg[yellow]%}%m%{$reset_color%} in %{$fg[green]%}%c%{$reset_color%} # %{$fg[blue]%}\${STY}%{$reset_color%} # %{$fg[blue]%}\$(git_prompt_info)%{$fg[blue]%} % %{$reset_color%}
	%{$fg[blue]%}➜ %{$reset_color%} "

	ZSH_THEME_GIT_PROMPT_PREFIX="%{$fg[cyan]%}"
	ZSH_THEME_GIT_PROMPT_SUFFIX="%{$reset_color%}"
	ZSH_THEME_GIT_PROMPT_DIRTY="%{$fg[blue]%} %{$fg[green]%}✗%{$reset_color%}"
	ZSH_THEME_GIT_PROMPT_CLEAN="%{$fg[blue]%}"

sjessa / dynamicsource.R

Created July 13, 2016 17:48

dynamically source a file in R

	# Source a file in the same directory as the script regardless of the
	# working directory from which the script is being called.
	# Works in conjunction with argparser.
	# Adapted from http://stackoverflow.com/a/1815743

	command <- commandArgs(trailingOnly = FALSE)
	script_name <- sub("--file=", "", command[grep("--file=", command)])
	script_path <- dirname(script_name)
	my_functions <- file.path(script_path, "functions.R")
	source(my_functions, chdir = TRUE)

sjessa / lmake.sh

Last active July 13, 2016 00:52

log your make commands & output

	# Usage: $ lmake <make options here> <optional make target>

	function lmake ()
	{
	echo "Appending make command output to make.log"
	echo "Running command..."

	echo "" >>make.log
	echo "------------------------------------------" >>make.log
	echo " MAKE LAUNCHED" >>make.log