.temp.Rmd

---
title: "Comparative Network Analyses"
author: "Alex Bartnik"
date: "April 30, 2019"
output: html_document
---

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

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r Load dependencies}

dependencies <- c(
  "dplyr",
  "tidyr",
  "ggplot2"
)

for (package in dependencies) {
  if (!package %in% (.packages())) {
    library(package,
            character.only = T)
  }
}

if (!exists("fcDev")) {
  source('../scripts/getData.R')
  source('../scripts/preprocessing.R')
}
source('../scripts/getNetworkConnections.R')

```

```{r}

setwd('/home/anacadmin/R/projects/scatters')
gatherAllPairsPerNetwork <- function(network.name) {
  
  internetworkpairs <- getInterNetworkPairs(getNetworkRegions(network.name))
  intranetworkpairs <- getIntraNetworkPairs(getNetworkRegions(network.name))

  subjects <- intersect(rownames(fcDev), rownames(dti))
  `Disease Group` <- disease.groups[subjects,]
  
  combinePairs <- function(inputData, source.name, inter.network, intra.network, disease.group) {
    rbind(
      cbind(inputData[subjects, inter.network], `Disease Group`) %>%
        mutate(subject = subjects) %>%
        gather(
          key = "pair",
          value = source.name,
          -subject, -`Disease Group`
        ) %>%
        mutate(location = "Internetwork"),
      cbind(inputData[subjects, intra.network], `Disease Group`) %>%
        mutate(subject = subjects) %>%
        gather(
          key = "pair",
          value = source.name,
          -subject, -`Disease Group`
        ) %>%
        mutate(location = "Intranetwork")
    ) %>%
      group_by(subject, location, `Disease Group`) %>%
      {
        if (source.name == "fcDev") {
          summarise(., fcDev = mean(source.name))
        } else if (source.name == "dti") {
          summarise(., dti = mean(source.name))
        }
      }
      
  }
  
  network.fcDev <- combinePairs(
    fcDev,
    "fcDev",
    getInterNetworkPairs(getNetworkRegions(network.name)),
    getIntraNetworkPairs(getNetworkRegions(network.name)),
    `Disease Group`
  )
  network.dti <- combinePairs(
    dti,
    "dti",
    getInterNetworkPairs(getNetworkRegions(network.name)),
    getIntraNetworkPairs(getNetworkRegions(network.name)),
    `Disease Group`
  )
  
  network <- merge(network.fcDev, network.dti)
  network.copy <- network
  network.copy$location = "All"
  network.all <- rbind(network, network.copy)
  
  return (network.all)
  
}

```

```{r}

setwd('/home/anacadmin/R/projects/scatters')
dmn <- gatherAllPairsPerNetwork("DMN")
auditory <- gatherAllPairsPerNetwork("Auditory")

```

```{r}

setwd('/home/anacadmin/R/projects/scatters/')
for (network in smith.networks) {
  
  if (network != "Cerbellum") {
    print(network)
    plotIntraNetworkSums(network, "Diffusion")
    ggsave(paste("Intranetwork",network,".png",sep=""),
           path = "figures/",
<<<<<<< HEAD
           width = 6,
           height = 5,
           dpi = 20)
=======
           width = 8,
           height = 6,
           dpi = 200)
>>>>>>> e9b41e2b074ab201b510e0c4b5358fc51b7af5d2
    
    plotInterNetworkSums(network, "Diffusion")
    ggsave(paste("Internetwork",network,".png",sep=""),
           path = "figures/",
<<<<<<< HEAD
           width = 6,
           height = 5,
           dpi = 20)
    
    plotNetworkSums(network, "Diffusion")
    ggsave(paste(network,".png",sep=""),
           path = "figures/",
           width = 6,
           height = 5,
           dpi = 20)
=======
           width = 10,
           height = 6,
           dpi = 200)
    
    plotNetworkSums(network, "Diffusion")
    ggsave(paste("WithinNetworkFC_",network,".png",sep=""),
           path = "figures/",
           width = 10,
           height = 6,
           dpi = 200)
    
    plotNetworkSums(network, "Diffusion", T)
    ggsave(paste("TotalFC_",network,".png",sep=""),
           path = "figures/",
           width = 10,
           height = 6,
           dpi = 200)
>>>>>>> e9b41e2b074ab201b510e0c4b5358fc51b7af5d2
  }
  
}

```

```{bash}

cd /home/anacadmin/R/projects/scatters/figures; ./montage.sh

```

```{r}

setwd('/home/anacadmin/R/projects/scatters/')
quickFacetPlot(dmn, "DMN", "Structural Disruption", "Change in Functional Connectivity")

```