Off Target Analysis

---
title: "Target RNAi Gene Regions for Vespa Velutina"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    social: menu
    source_code: embed
---

```{r setup, include=FALSE}
library(knitr)
library(d3heatmap)
library(flexdashboard)
library(tidyr)
library(dplyr)
library(ggplot2)
library(stringr)
```




# Off Target Analysis
```{r}
CHS<-read.table("/home/saisha/Desktop/unil_igem/01.Chitin-Synthase/03.off_targets/blast_results.txt",sep = "\t", header = TRUE, check.names = FALSE,comment.char = "")
CHS$stitle<-sub("^(([^ ]+ ){2}).*", "\\1", CHS$stitle)
```



### Stats per Target Region {data-width=1050, data-height=950}

```{r}
CHS  %>%
    group_by(qseqid)  %>% mutate(num_species=n_distinct(stitle)) %>% ungroup %>% group_by(qseqid, stitle) %>%
    mutate(score = max(bitscore), mpident = max(pident), mismatch=max(mismatch),gap=max(gapopen) )%>%  filter(num_species<10) %>% select(qseqid, stitle, score) %>%  # Select relevant columns
    distinct(qseqid, stitle, score) %>%
    pivot_wider(names_from = stitle, values_from = score, values_fill = 0) %>%  # Pivot data to wide format
    tibble::column_to_rownames(var = "qseqid") %>% d3heatmap(scales="column",col = "Blues")


```



### Top Genes {data-width=350}

```{r}
Table<-CHS  %>%
    group_by(qseqid)  %>% mutate(num_species=n_distinct(stitle)) %>% ungroup %>% group_by(qseqid, stitle) %>%
    mutate(score = max(bitscore), mpident = max(pident), mismatch=max(mismatch),gap=max(gapopen) )%>%  
    filter(num_species<10) %>% select(qseqid, stitle, score) %>%
    separate(qseqid, c('qseqid', 'GC',"AC"),sep = "\\|") 


Table$GC<-as.numeric(sub("GC:", "",Table$GC))
Table$AC<-as.numeric(sub("AC:", "",Table$AC))

knitr::kable(Table)
```