dgrapov

library(shiny)
library(ggvis)

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

dgrapov

---
title: "Hands-on with dplyr"
author: "Dmitry Grapov"
output:
  html_document:
    keep_md: yes
---

## Introduction

dgrapov

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

Name	KEGG id
Carnitine	C00318
catechin	C06562
threonine	C00188
threonic acid	C01620
phenylethylamine	C05332
phenylalanine	C00079
N-acetyl-L-ornithine	C00437
mannitol	C00392
glutathione	C00051

dgrapov

#------------------------------------------------------
# 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)

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#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

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

# Script to demonstrate distributions
library(VGAM)
library(eeptools)
library(shiny)
library(ggplot2)
 
 
 
 
shinyServer(function(input,output){

dgrapov

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

#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)