ovcarChibe.Rmd

---
title: "Generate Causality SIF"
output:
  html_document:
    toc: yes
  pdf_document:
    toc: yes
---

```{r setup, echo=FALSE, warning=FALSE, message=FALSE}
require("knitr")
opts_knit$set(root.dir="..")
opts_chunk$set(fig.align="center", fig.width=6, fig.height=6, dpi=300)

```

## Purpose
* Plot SIFs generated by the Causality analysis

## Setup 
```{r loadLibraries, message=FALSE, warning=FALSE}
library(zeptosensPkg)
library(paxtoolsr)
library(igraph)
```

## Generate SIF File
```{r}
graphType <- "compatible"
signedPcDir <- tempdir()
siteMatchStrict <- TRUE
resultPrefix <- "inst/ovcarProject/ovcar3_dif_drug_sig_"
platformFile <- "inst/chibeExample/abdata-chibe.txt"
valuesFile <- file.path(.googleDrive, "ovcar_project/ozgun_data/ozgun_data/dif_drug_sig/ovcar3_dif_drug_sig.txt")
geneCentric <- TRUE

compatibleResults <- generateRPPAGraphs(platformFile = platformFile, 
                              idColumn = "ID1", 
                              symbolsColumn = "Symbols",  
                              sitesColumn = "Sites",
                              effectColumn = "Effect", 
                              valuesFile = valuesFile, 
                              valueColumn = "change", 
                              valueThreshold = 0.001,
                              graphType = graphType, 
                              siteMatchStrict=siteMatchStrict,
                              geneCentric=geneCentric,
                              outputFilePrefix = paste0(resultPrefix, "compatible"),
                              customNetworkDirectory=signedPcDir)

compatibleSif <- compatibleResults$sif
compatibleSif[, "graphType"] <- rep(graphType,  nrow(compatibleResults$sif))

graphType <- "conflicting"
conflictingResults <- generateRPPAGraphs(platformFile = platformFile, 
                              idColumn = "ID1", 
                              symbolsColumn = "Symbols",  
                              sitesColumn = "Sites",
                              effectColumn = "Effect", 
                              valuesFile = valuesFile, 
                              valueColumn = "change", 
                              valueThreshold = 0.001,
                              graphType = graphType, 
                              siteMatchStrict=siteMatchStrict,
                              geneCentric=geneCentric,
                              outputFilePrefix = paste0(resultPrefix, "conflicting"),
                              customNetworkDirectory=signedPcDir)

conflictingSif <- conflictingResults$sif
conflictingSif[, "graphType"] <- rep(graphType,  nrow(conflictingResults$sif))

overallSif <- rbind(conflictingSif, compatibleSif)
overallSif <- unique(overallSif)

write.table(overallSif, file=paste0(resultPrefix, "overall.sif"), sep="\t", row.names=FALSE, quote=FALSE, na="")
```

## Combine SIF
```{r}
#cat ovcar3_dif_drug_sig_compatible.sif ovcar3_dif_drug_sig_conflicting.sif > ovcar3_dif_drug_sig_overall.sif
#cat ovcar3_dif_drug_sig_compatible.format ovcar3_dif_drug_sig_conflicting.format > ovcar3_dif_drug_sig_overall.format

conflictingSif <- read.table(paste0(resultPrefix, "conflicting.sif"), sep="\t", fill=TRUE, row.names=NULL, header=FALSE, stringsAsFactors=FALSE)
compatibleSif <- read.table(paste0(resultPrefix, "compatible.sif"), sep="\t", fill=TRUE, row.names=NULL, header=FALSE, stringsAsFactors=FALSE)

if(ncol(compatibleSif) == 4) {
    compatibleSif <- cbind(compatibleSif, "V5"=rep(NA, nrow(compatibleSif)))
}

if(ncol(conflictingSif) == 4) {
    conflictingSif <- cbind(conflictingSif, "V5"=rep(NA, nrow(conflictingSif)))    
}

overallSif <- rbind(as.matrix(compatibleSif), as.matrix(conflictingSif))
overallSif <- unique(overallSif)

write.table(overallSif, file=paste0(resultPrefix, "overall.sif"), 
            sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE, na="")

conflictingFormat <- read.table(paste0(resultPrefix, "conflicting.format"), sep="\t")
compatibleFormat <- read.table(paste0(resultPrefix, "compatible.format"), sep="\t")

conflictingFormat$V4 <- sub("0 100 0", "0 255 255", conflictingFormat$V4)
conflictingFormat$V4 <- sub("100 0 0", "255 0 255", conflictingFormat$V4)

# Only merge edge data
overallFormat <- rbind(compatibleFormat, conflictingFormat[conflictingFormat$V1 == "edge", ])
write.table(overallFormat, file=paste0(resultPrefix, "overall.format"), 
            sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE, na="")
```

## Parse Causality SIF 
```{r}
# Get results to plot
causalityResults <- conflictingResults
g <- generateCausalityIgraph(causalityResults)

plot(g, layout=layout.fruchterman.reingold, 
     edge.arrow.width=0.5, edge.arrow.size=0.5, edge.color=E(g)$color, edge.lty=E(g)$lty,
     vertex.color=V(g)$color, vertex.label.cex=0.5)
```

## Session Info

```{r, eval=FALSE}
sessionInfo()
```