---
title: "21-compare-across"
output: html_document
date: "2025-07-21"
---
Rmd to compare the immune-related transcripts across species and create tables of transcripts that are shared and unique across the three species at Day 12. 

```{r}
library(tidyverse)
library(dplyr)
```

Read in the three annotated immune short list transcript tables: 

```{r}
pyc <- read.delim("../output/18-annot-pycno/Phel_immune_shortlist.txt")
head(pyc)
```

```{r}
pis <- read.delim("../output/19-annot-pisaster/Pisaster_immune_shortlist.txt")
head(pis)
```

```{r}
derm <- read.delim("../output/20-annot-derm/Derm_immune_shortlist.txt")
head(derm)
```

```{r}
derm_unique <- derm[!duplicated(derm), ] %>% distinct(Entry, .keep_all = TRUE)
```

```{r}
pyc_unique <- pyc[!duplicated(pyc), ] %>% distinct(Entry, .keep_all = TRUE)
```

```{r}
pis_unique <- pis[!duplicated(pis), ] %>% distinct(Entry, .keep_all = TRUE)
```

# `join` all three tables by "Entry"

```{r}
allthree <- pyc_unique %>% 
  inner_join(pis_unique, by = "Entry") %>% 
  inner_join(derm_unique, by = "Entry")
```


write out table:
```{r}
write.table(allthree, "../output/21-compare-across/All_three_species_immune_shortlist.tab", sep = "\t", row.names = FALSE, quote = FALSE, col.names = TRUE)
```