AliciaSchep’s gists

AliciaSchep / git-branches-by-commit-date.sh

Created April 22, 2019 17:34 — forked from jasonrudolph/git-branches-by-commit-date.sh

List remote Git branches and the last commit date for each branch. Sort by most recent commit date.

	# Credit http://stackoverflow.com/a/2514279
	for branch in `git branch -r \| grep -v HEAD`;do echo -e `git show --format="%ci %cr" $branch \| head -n 1` \\t$branch; done \| sort -r

AliciaSchep / cute_email_gadget.R

Created April 14, 2019 16:24

Shiny Gadget For Emailing Cute Puppies

	library(shiny)
	library(miniUI)
	library(gmailr)
	library(rtweet)
	library(purrr)

	use_secret_file("~/client_id.json")

	send_email <- function(to_address, picture_url, msg = "",
	subject = "Cute Picture", expanded_url = picture_url){

AliciaSchep / plotly_dropdown_example.R

Created April 14, 2019 16:20

Plotly Dropdown Example

	p <- plot_ly(mtcars, x = ~wt) %>%
	add_markers(y = ~mpg, name = "A") %>%
	add_markers(y = ~hp, name = "B", visible = F) %>%
	layout(
	title = "Drop down menus - Update",
	xaxis = list(domain = c(0.1, 1)),
	yaxis = list(title = "mpg"),
	updatemenus = list(
	list(
	y = 0.7,

AliciaSchep / deploy_to_gh_pages.r

Last active March 9, 2019 18:10

Deploy a pkgdown site to gh_pages branch

	## Adapted from r-lib/pkgdown source code from RStudio https://github.com/r-lib/pkgdown

	## Helper functions, directly from pkgdown code --------------------------------
	git <- function(...) {
	processx::run("git", c(...), echo_cmd = TRUE, echo = TRUE)
	}

	github_clone <- function(dir, repo_slug) {
	remote_url <- sprintf("[email protected]:%s.git", repo_slug)
	cli::rule("Cloning existing site", line = 1)

AliciaSchep / event_listener_bug_example.Rmd

Created April 12, 2018 05:01

Example document showcasing a bug with inappropriate insertion of wheel event listener by rstudio in rmarkdown inline view / notebook

	---
	title: "event listener bug"
	author: "Alicia Schep"
	date: "April 11, 2018"
	output: html_document
	---

	```{r setup, include=FALSE}
	knitr::opts_chunk$set(echo = TRUE)
	```

AliciaSchep / get_libs_used.r

Created February 19, 2018 07:17

Find the r packages used in directory

	get_r_files <- function(path = ".", recursive = FALSE, include_rmd = TRUE){
	all_files <- normalizePath(list.files(path, full.names = TRUE,
	recursive = recursive))

	r_files <- grep(".*\\.(r\|R)$", all_files, value = TRUE)

	if (include_rmd){
	r_files <- c(r_files,
	grep(".*\\.(r\|R)md$", all_files, value = TRUE))
	}

AliciaSchep / fresh_r_libraries.r

Created February 19, 2018 06:01

Setup use of a new, fresh library directory in R

	create_lib_dir <- function(name, path = "."){

	dir_path <- file.path(path, name)
	if (!dir.exists(dir_path)) {
	message("Creating new dir: ", dir_path)
	dir.create(dir_path)
	}

	normalizePath(dir_path)
	}

AliciaSchep / simpelist_coercion_example.r

Created November 30, 2017 05:04

AliciaSchep / get_footprint.R

Created November 30, 2017 04:54

Compute aggregate footprint around position

	library(GenomicRanges)
	library(S4Vectors)

	# Footprint does not include +/- 4 correction for ATAC-seq

	# Modified tabulate funcion ----------------------------------------------------

	tabulate2 <- function(x, min_val, max_val) {
	if (max_val <= min_val) {
	stop("max_val must be greater than min_val")

AliciaSchep / complex_layout.json

Created November 19, 2017 05:07

vegalite hconcat plus vconcat plus layer

	{
	"$schema": "https://vega.github.io/schema/vega-lite/v2.json",
	"description": "Two horizonally concatenated charts that show a histogram of precipitation in Seattle and the relationship between min and max temperature.",
	"data": {
	"url": "data/weather.csv",
	"format": {
	"type": "csv"
	}
	},
	"transform": [

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