UpSetR_script.Rmd

---
title: "intersection_script"
author: "Morgan Chunn"
output: html_document
 
---

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

# Loading packages 
```{r}
if (!require("UpSetR")) install.packages("UpSetR"); library(UpSetR)
```


# all genes.. boolean data file 
```{r}
dat <- read.csv("countsFileBoolean.csv", header=T, row.names = 1)
head(dat)
```

# plot showing intersections between all species/all genes 
```{r}
upset(dat, nsets =12 , number.angles = 30, point.size = 2, line.size = 1, 
      mainbar.y.label = "Gene Intersection Size", 
      text.scale = c(1, 1, 1, 1, 0.75, 0.75))
```

# plot showing intersections between specfic speices (Frugivore/Piscivore)
```{r}

upset(dat, sets = c("nole_p", "stlu_f", "chvi_f"), sets.bar.color = "#56B4E9",
order.by = "freq", empty.intersections = "on", mainbar.y.label = "Gene Intersections" , query.legend = "top", queries = list(list(query = intersects, params = list("stlu_f","chvi_f"), color = "orange", active = T, query.name = "Frugivores"), (list(query = intersects, params = list("nole_p","chvi_f"), color = "red", active = T, query.name = "Frugivore/Piscivore"))))

```

# plot showing intersections between specfic speices (Frugivore/Insectivore)
### top three intersection groups were between frugivores. 
```{r}

upset(dat, sets = c("stlu_f", "mawa_i", "arja_f", "chvi_f"), sets.bar.color = "#56B4E9",
order.by = "freq", empty.intersections = "on", mainbar.y.label = "Gene Intersections", queries = list(list(query = intersects, params = list("stlu_f", "arja_f", "chvi_f"), color = "orange", active = T),list(query = intersects, params = list("stlu_f","arja_f"), color = "orange", active = T),list(query = intersects, params = list("stlu_f","chvi_f"), color = "orange", active = T), (list(query = intersects, params = list("stlu_f","chvi_f", "mawa_i"), color = "red", active = T))))


```

# plot showing intersections between specfic speices (Frugivore/Insectivore) and presence specifc gene 
```{r}
func <- function(row, species) {
    dat <- (row["gene"] %in% species) 
}

upset(dat, sets = c("nole_p", "stlu_f", "chvi_f"), sets.bar.color = "#56B4E9",
order.by = "freq", empty.intersections = "on", mainbar.y.label = "Gene Intersections" , query.legend = "top", queries = list(list(query = func, params = list(1534), color = "blue", active = F, query.name = "specific gene"),list(query = intersects, params = list("stlu_f","chvi_f"), color = "orange", active = T, query.name = "Frugivores"), (list(query = intersects, params = list("nole_p","chvi_f"), color = "red", active = T, query.name = "Frugivore/Piscivore"))))
    
```