upsetter.Rmd

---
title: "Upsetter plot with all phenotypes"
author: "Briana Mittleman"
date: "1/7/2020"
output: html_document
---

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

In this analysis I will use the UpSetR package to look at all of the differential gene regulation phenotype results in one plot. This should be easier to visualize than the venn diagrams.  


```{r}

library(UpSetR)
library(workflowr)
library(tidyverse)
```



Input the datasets:

```{r}
#protein
Protein=read.table("../data/Khan_prot/HC_SigProtein.txt", header = T, stringsAsFactors = F)
#trans
Translation=read.table("../data/Wang_ribo/HC_SigTranslation.txt", header = T, stringsAsFactors = F)
#expression
nameID=read.table("../../genome_anotation_data/ensemble_to_genename.txt",sep="\t", header = T, stringsAsFactors = F)
DEgenes=read.table("../data/DiffExpression/DE_genes.txt", header = F,col.names = c("Gene_stable_ID"),stringsAsFactors = F) %>% inner_join(nameID, by="Gene_stable_ID") %>% dplyr::select(Gene.name)
#nuclear apa  
NucAPA=read.table("../data/DiffIso_Nuclear/SignifianceEitherGENES_Nuclear.txt",header = T,stringsAsFactors = F)
#totalAPA  
totAPA=read.table("../data/DiffIso_Total/SignifianceEitherGENES_Total.txt",header = T,stringsAsFactors = F)
DSgenes=read.table("../data/DiffSplice_liftedJunc/orderedGeneListFixed.txt",stringsAsFactors = F, col.names = "DS")

```


Create a named list object  

```{r}
# example of list input (list of named vectors)
listInput <- list(DE=DEgenes$Gene.name, DS=DSgenes$DS, DapaNuc=NucAPA$gene, DapaTot=totAPA$gene, DT=Translation$Gene, DP=Protein$gene.symbol)

```


Create plot:

```{r}
upset(fromList(listInput), order.by = "freq", keep.order = T,empty.intersections = "on")
```

Do this without total APA:  

```{r}
listInput_nucOnly <- list(DE=DEgenes$Gene.name, DS=DSgenes$DS, DAPA=NucAPA$gene, DT=Translation$Gene, DP=Protein$gene.symbol)

upset(fromList(listInput_nucOnly), order.by = "freq", keep.order = T,empty.intersections = "on")
```

Add colors for certain queries:

```{r}
#upset(movies, queries = list(list(query = intersects, params = list("Drama", 
#    "Comedy", "Action"), color = "orange", active = T), list(query = intersects, 
 #   params = list("Drama"), color = "red", active = F), list(query = intersects, 
 #   params = list("Action", "Drama"), active = T)))


upset(fromList(listInput_nucOnly), queries = list(list(query=intersects, params=list("DAPA", "DT", "DP"), color="red", active=T,query.name="APA,Ribo, Protein"),list(query=intersects, params=list("DE", "DT", "DP"), color="orange", active=T, query.name="Expression,Ribo, Protein"), list(query=intersects, params=list("DS", "DT", "DP"), color="green", active=T,query.name="Splicing ,Ribo, Protein"),list(query=intersects, params=list("DAPA", "DT"), color="blue", active=T, query.name="APA,Ribo") ,list(query=intersects, params=list("DAPA", "DP"), color="purple", active=T, query.name="APA, Protein")), order.by = "freq", query.legend = "bottom")

```


**Can I do this by proportion???**