Dmitry Grapov dgrapov

Biotechnology, data, math, art and code.

dgrapov / app

Last active August 29, 2015 14:20

ggvis linked brushing bug

	library(shiny)
	library(ggvis)

	shinyApp(
	ui =bootstrapPage(
	actionButton("randomize", "Randomize"),
	ggvisOutput("plot1"),
	ggvisOutput("plot2"),
	verbatimTextOutput("summary")
	),

dgrapov / dplyr_tutorial.Rmd

Created April 28, 2015 23:21

hands on with dplyr

dgrapov / oxylipins edge list

Last active August 29, 2015 14:02

edge list for making oxylipin networks (partial)

	sourceName sourceKEGG sourceCID targetName targetKEGG targetCID indirect
	arachidonic_acid C00219 444899 TXB2 C05963 5283137 y
	arachidonic_acid C00219 444899 PGE2 C00584 5280360 y
	arachidonic_acid C00219 444899 LTB4 C02165 5280492 y
	linoleic_acid C01595 5280450 9,10,13-TriHOME C14835 5282965 y
	linoleic_acid C01595 5280450 9,12,13-TriHOME C14833 9858729 y
	linoleic_acid C01595 5280450 EKODE 5283007 y
	arachidonic_acid C00219 444899 11(12)-EpETrE 53480479 n
	arachidonic_acid C00219 444899 11-HETE C14780 5283168 n
	arachidonic_acid C00219 444899 12-HETE C14777 5283155 n

dgrapov / mapping test set

Created April 14, 2014 16:15

Test data set for ID translation

dgrapov / correlation edge list

Last active August 29, 2015 13:57

Making edge lists for correlation networks

	#------------------------------------------------------
	# demonstration of making edge lists for
	# correlation network analysis
	# by Dmitry Grapov
	# 031814
	#------------------------------------------------------

	# load devium library for all functions
	source("http://pastebin.com/raw.php?i=JVyTrYRD") # sources function to download github repo (https://github.com/dgrapov/devium)

dgrapov / Data Summaries and Tests

Created November 12, 2013 17:13

Example of data summary tools.

	#demonstration of data summary tools
	#enable necessary functions
	source("http://pastebin.com/raw.php?i=JVyTrYRD")

	#get demo data
	library(RCurl)
	url<-getURL("https://docs.google.com/spreadsheet/pub?key=0Ap1AEMfo-fh9dGFHRk81cVJaMTIxUjQzSlo2RS1RZXc&single=true&gid=0&output=csv",ssl.verifypeer = FALSE)
	tmp.data<-read.csv(textConnection(url))

	#Prepare to generate data summaries and conduct statitcal tests

dgrapov / server.R

Last active December 20, 2015 14:39

compare skewed to normal distrubution

	shinyServer(function(input,output){
	mydat <- reactive(function() {
	scale(rsnorm(input$obs, location = input$mean, scale =input$variance,
	shape = input$skew),center=TRUE,scale=TRUE)
	})

	ndat <- reactive(function() {
	scale(rnorm(input$obs, mean = input$mean, sd =input$variance),center=TRUE, scale=TRUE)
	})

dgrapov / server.R

Last active December 20, 2015 14:29 — forked from jknowles/server.R

	# Script to demonstrate distributions
	library(VGAM)
	library(eeptools)
	library(shiny)
	library(ggplot2)




	shinyServer(function(input,output){

dgrapov / server.r

Last active October 24, 2016 12:43

Testing Shiny input text area. Based on http://stackoverflow.com/questions/14452465/how-to-create-textarea-as-input-in-a-shiny-webapp-in-r. Need to put .js in www folder.

	shinyServer(function(input, output, session) {
	inputTextarea <- function(inputId, value="", nrows, ncols) {
	tagList(
	singleton(tags$head(tags$script(src = "textarea.js"))),
	tags$textarea(id = inputId,
	class = "inputtextarea",
	rows = nrows,
	cols = ncols,
	as.character(value))
	)

dgrapov / query PubMed

Last active December 19, 2015 00:48

Check for key word in PubMed article titles

	#Check pubmed article titles for a given year for a keyword (using partial matching).

	library(XML)
	library(stringr)


	#get PubMed Ids for all journals for a given year
	getPubMedIds<-function(year=2013, max=100){
	#max = maximum results to return
	url<-paste0("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=",year,"[PDAT]&RetMax=",max)