cascade_to_sif.Rmd

---
title: "Cascade file (Signor .tsv format) to topology (.sif)"
author: "[John Zobolas](https://github.com/bblodfon)"
date: "Last updated: `r format(Sys.time(), '%d %B, %Y')`"
output:
  html_document:
    theme: united
    number_sections: false
    code_folding: show
    code_download: true
---

With the code below we translate the `cascade_2.0.tsv` file (or any Signor-based 
interactions .tsv format file) to a single interactions file (`cascade_2.0.sif`).

```{r Input Singor data, comment=""}
# load cascade file
cascade.file = "cascade_2.0.tsv"
entries = read.table(file = cascade.file, header = TRUE, sep = "\t", 
                     comment.char = "", stringsAsFactors = FALSE)

# format of columns is Signor based (.tsv output)
colnames(entries)
```

```{r Output SIF file}
# check that ENTITYA, ENTITYB, EFFECT columns are not empty for any interaction
entity.A = entries["ENTITYA"]
entity.B = entries["ENTITYB"]
effect = entries["EFFECT"] # inhibit or activate

causal.entries = cbind(entity.A, entity.B, effect)
  
stopifnot(all(sum(entity.A != "")))
stopifnot(all(sum(entity.B != "")))
stopifnot(all(sum(effect != "")))

# add effect annotation
effect.annot = apply(causal.entries, 1, function(entry) {
  if (entry[3] == "activate") return("->")
  else if (entry[3] == "inhibit") return("-|")
  else stop("effect column value is neither activate nor inhibit")
})

causal.entries = cbind(causal.entries, effect.annot)

# remove EFFECT column
causal.entries = causal.entries[c("ENTITYA","effect.annot","ENTITYB")]

# output to file (seperator: space)
topology.file = "cascade_2.0.sif"
write.table(x = causal.entries, file = topology.file, quote = FALSE, 
            col.names = FALSE, row.names = FALSE, sep = " ")
```

```{r Report number of nodes and edges from .sif topology file, comment=""}
interactions = read.table(file = topology.file)

num.of.interactions = nrow(interactions)
sources = as.character(interactions[, 1])
targets = as.character(interactions[, 3])

nodes = unique(c(sources, targets))
num.of.nodes = length(nodes)

print(paste0("File: ", topology.file, " has ", num.of.nodes, " nodes",
  " and ", num.of.interactions, " interactions"))
```