fastgear_recent_recombinations.Rmd

---
title: "R Notebook"
output: html_notebook
---



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

```{r}
recombinations_recent <- read.csv("~/Documents/2021-Fiji-Ct_paper/fastGEAR_withGlobal_189/recombinations_recent.txt", sep="") %>%
  mutate(Length = End-Start+1)
```

# The Fiji strains are indexed as 1-82

# putative recombination events from Ocular
```{r}
recombinations_recent %>% 
  filter(DonorLineage == 1) %>%
  filter(RecipientStrain < 83) %>%
  group_by(DonorLineage,log.BF.,Start,End,Length) %>%
  summarise(y = list(StrainName)) %>%
  unnest_wider(y)
```

# putative recombination events from LGV
```{r}
recombinations_recent %>% 
  filter(DonorLineage == 2) %>%
  filter(RecipientStrain < 83) %>%
  group_by(DonorLineage,log.BF.,Start,End,Length) %>%
  summarise(y = list(StrainName)) %>%
  unnest_wider(y)
```

# table of all recombinations and which strain is involved

```{r}
fiji_recombs <- recombinations_recent %>% 
  filter(RecipientStrain < 83) %>%
  group_by(DonorLineage,Start,End,Length) %>%
  summarise(y = list(StrainName)) %>%
  unnest_wider(y)

write_tsv(fiji_recombs,"fastgear_fiji_recombs")
```


```{r}
fiji_recombs_count <- recent_reomb %>% 
  filter(RecipientStrain < 83) %>%
  group_by(DonorLineage,Start,End,Length) %>%
  tally()
```

```{r}
ggplot(fiji_recombs_count,aes(n)) + 
    geom_histogram(binwidth=1) +
    ggtitle("Number of strains in each recombination event") +
    theme_bw()
```
Looks at where the strain specific recombination events fall
```{r}
ggplot(filter(fiji_recombs_count,n == 1),aes(Start)) + 
    geom_histogram(binwidth=10000) +
    ggtitle("Start site of strain specific recombinations") +
    xlim(1,1042519) +
    ylim(0,5) +
    theme_bw()
```
```{r}
fiji_recombs_count %>%
  filter(n > 2) %>%
  arrange(Start)
```
Lineage 1 = LGV; Lineage 2 = trachoma