Thomas Falk reinholdsson

Bioconductor Shiny Example #3

Simple app showing the relationship between a gene's expression and survival.

This is an example Shiny app featuring some basic analysis of Ovarian Cancer gene expression data collected on the Affymetrix U133A platform. We filter the available genes and samples down to a much smaller matrix to make reproducibility simpler for a broader audience. The R code involved in sampling the data is available in this Gist as an R-Markdown file, and the sampled data are available in this Gist as Rds files.

To run the application, install shiny (install.packages("shiny")) then run the following command:

library(shiny)

Slidify now allows you to publish your slide decks as gists. You will need the dev version of slidify to use this feature.

require(devtools)
install_github(c('slidify', 'slidifyLibraries'), 'ramnathv', ref = 'dev')

Let us first create a directory for our slide deck and open an index.Rmd file to author our presentation.

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Highly recommended things!

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A few of these works have had an extraordinary effect on my life or way of thinking. They get a sixth star. ★

	from bubbles import Pipeline, open_store

	stores = {
	"source": open_store("csv", "data/source", encoding="utf16", infer_fields=True),
	"target": open_store("sql", "sqlite:///data.sqlite")
	}

	p = Pipeline(stores=stores)

	# Load customers into a SQL table

	#!/usr/bin/Rscript

	require(knitr)
	lf <- commandArgs(trailingOnly = TRUE)
	if(!length(lf))
	lf = list.files(pattern="\\.rmd")
	for (f in lf)
	try(knit(f))

	md = paste0(sub("\\.[[:alnum:]]*$", "", lf), ".md")

	.Rproj.user
	.Rhistory
	.RData
	*.Rproj
	*.html

	def shellout(template, **kwargs):
	"""
	Takes a shell command template and executes it. The template must use
	the new (2.6+) format mini language. `kwargs` must contain any defined
	placeholder, only `output` is optional.
	Raises RuntimeError on nonzero exit codes.

	Simple template:

	wc -l < {input} > {output}

	# Helper functions that allow string arguments for dplyr's data modification functions like arrange, select etc.
	# Author: Sebastian Kranz

	# Examples are below

	#' Modified version of dplyr's filter that uses string arguments
	#' @export
	s_filter = function(.data, ...) {
	eval.string.dplyr(.data,"filter", ...)
	}

	## GUIDE TO AUTH2 Authentication in R Shiny (or other online apps)
	##
	## Mark Edmondson 2015-02-16 - @HoloMarkeD \| http://markedmondson.me
	##
	## v 0.1
	##
	##
	## Go to the Google API console and activate the APIs you need. https://code.google.com/apis/console/?pli=1
	## Get your client ID, and client secret for use below, and put in the URL of your app in the redirect URIs
	## e.g. I put in https://mark.shinyapps.io/ga-effect/ for the GA Effect app,

	#!/usr/bin/env python3
	"""
	Running this script is (intended to be) equivalent to running the following Snakefile:

	include: "pipeline.conf" # Should be an empty file

	shell.prefix("set -euo pipefail;")

	rule all:
	input: