oganm

extendShinyjsEvenFurther = function(){
    jscode <- '
Shiny.addCustomMessageHandler("mymessage", function(message) {
    eval(message);
});
    '
    tags$head(tags$script(HTML(jscode)))
}

jsExecute = function(jscode,session){

oganm

library(shiny)
library(shinyWidgets)

moduleUI = function(id){
    ns = NS(id)
    
    tagList(actionButton(inputId = ns('update'),label = 'update'),
            progressBar(id = "progressBar", value = 50),
            checkboxInput(inputId = ns('checkbox'),label = 'shinyCheckbox',value = FALSE))
}

oganm

# ontologyPlot package requires bioconductor package Rgraphvis
# source("https://bioconductor.org/biocLite.R")
# biocLite("Rgraphvis")
# install.packages('ontologyIndex')
# install.packages('ontologyPlot')

library(ontologyIndex)
library(ontologyPlot)

download.file(url = 'http://purl.obolibrary.org/obo/uberon.obo',destfile = 'uberon.obo')

oganm

library(CellCODE)
library(dplyr)
library(purrr)
library(magrittr)
library(markerGeneProfile)
data('mouseMarkerGenesCombined')

# this function will turn gene lists into CellCODE inputs
cellCodeInput = function(genes){
    geneCount = genes %>% map(length)

oganm

library(stringr)
library(magrittr)
library(pdftools)
library(Hmisc)

capitalizeAll = function(x){
    words = strsplit(x, ' ') %>% {.[[1]]}
    capital = sapply(words, function(x){
        if(x %in% c('for','of','and','to','into','with','the','from','via')){
            return(x)

oganm

// Browser fingerprinting is a technique to "mark" anonymous users using JS
// (or other things).  To build an "identity" of sorts the browser is queried
// for a list of its plugins, the screen size and several other things, then
// hashes them.  The idea is that these bits of information produce an unique
// "fingerprint" of sorts; the more elaborate the list of data points is, the
// more unique this fingerprint becomes.  And you wouldn't even need to set a
// cookie to recognize this user when she visits again.
//
// For more information on this topic consult
// [Ars Technica](http://arstechnica.com/tech-policy/news/2010/05/how-your-web-browser-rats-you-out-online.ars)

oganm

regions = c('Cortex','Hippocampus','Striatum','Cerebellum','Thalamus')


regions %>% lapply(function(x){
    cellTypes = names(mouseMarkerGenesCombined[[x]])
    cellTypes %>% lapply(function(y){
        data.frame(symbol = mouseMarkerGenesCombined[[x]][[y]], NCBIid = mouseMarkerGenesCombinedNCBI[[x]][[y]])
    })

})

oganm

library(import5eChar)
library(purrr)
library(ogbox)
library(dplyr)
library(ggplot2)
library(stringr)
library(igraph)
library(glue)
library(cowplot)
charFiles = c(list.files('/srv/shiny-server/printSheetApp/chars/',full.names = TRUE),

oganm

library(magrittr)
library(dplyr)
library(homologene) 
library(gemmaAPI) #  github.com/pavlidisLab/gemmaAAPI.R
library(markerGeneProfile) # github.com/pavlidisLab/markerGeneProfile
data("mouseMarkerGenesCombined")

# get mouse homologues of the hitlist
hitlist = readxl::read_xlsx('gene of interest.xlsx',col_names = FALSE) %>% 
  unlist %>% human2mouse %$% mouseGene

oganm

getGithubFile = function(githubPath,branch = 'master', downloadPath = NULL,token = NULL){
    if(is.null(downloadPath)){
        downloadPath = tempfile()
    }
    
    path = strsplit(githubPath,'/')[[1]]
    file = paste(path[3:length(path)], collapse = '/')
    contents = gh::gh('GET /repos/:username/:reponame/contents/:dir?ref=:branch',
                  username = path[1],
                  reponame = path[2],