index.Rmd

---
title: "AvcD Homologs"
---

```{r setup, eval=TRUE, echo=FALSE, include=FALSE, warning=FALSE}
library(tidyverse)
library(here)
# library(shiny); library(shinydashboard); library(flexdashboard)
library(DT)
library(fontawesome)
```

# A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection
`r fa("quote-left", fill = "darkred")` [How to Cite](cite.html) <br>

***

## Explore the AvcD homologs and their descriptions below
You can search, sort, and query the table interactively.
In addition, you can show/hide specific columns using the `Column visibility` button.

```{r load_data, eval=TRUE, echo=FALSE, include=FALSE, warning=FALSE}
infile_blast <- here("../molevol_data/project_data/phage_defense/full_analysis_20210108/cln_combined_uniq.tsv")
blast_combnd <- read_tsv(infile_blast, col_names=T) %>%
  mutate(QueryName=Query)
blast_combnd$Query <- blast_combnd %>%
  pull(QueryName) %>%
  str_replace_all(pattern = "WP_001901328.1",
                  replacement = "Vcholerae") %>% #Vcholerae_WP_001901328.1
  str_replace_all(pattern = "WP_020839904.1",
                  replacement = "Vparahaemolyticus") %>% #Vparahaemolyticus_WP_020839904.1
  str_replace_all(pattern = "WP_096882215.1",
                  replacement = "Ecoli") %>% #Ecoli_WP_096882215.1
  str_replace_all(pattern = "WP_108717204.1",
                  replacement = "Pmirabilis") %>% #Pmirabilis_WP_108717204.1
  str_replace_all(pattern = "WP_043825948.1",
                  replacement = "Averonii") %>% #Averonii_WP_043825948.1
  str_replace_all(pattern = "WP_129996984.1",
                  replacement = "Ecloacae") #Ecloacae_WP_129996984.1
```

```{r table, eval=TRUE, echo=FALSE, warning=FALSE}

# selectInput("QueryName", "Query:",
#             c("V. cholerae"="Vcholerae_WP_001901328.1",
#               "V. parahaemolyticus"="Vparahaemolyticus_WP_020839904.1",
#               "E. coli"="Ecoli_WP_096882215.1",
#               "P. mirabilis"="WP_108717204.1_Proteus_mirabilis",
#               "A. veronii"="Averonii_WP_043825948.1",
#               "E. cloacae"="Ecloacae_WP_129996984.1"))

blast_combnd <- blast_combnd %>%
  select(Name, Lineage, Species,
  			 Query, PcPositive, AccNum, ProteinName,
         DomArch.Gene3D, DomArch.Pfam,
         DomArch.PANTHER, DomArch.Phobius) %>%
	arrange(-PcPositive, Name) %>%
	filter(!is.na(Species)) %>% filter(!is.na(Lineage))

# blast_combnd %>%
# 	filter(QueryName==input$QueryName) %>%
# 	rmarkdown::paged_table()

DT::datatable(blast_combnd, extensions = c('Buttons', 'FixedColumns', 'RowReorder'),
							options = list(
	pageLength = 10,
	dom = 'Bfrtip',
	#buttons = I('colvis'),
	buttons=list(list(extend = 'colvis', columns = c(3:11))),
	fixedColumns = list(leftColumns = 2), #, rightColumns = 1),
	rowReorder = TRUE, order = list(c(0, 'asc')),
	scrollX = TRUE,
	lengthMenu = c(10, 25, 100)
))


# output$blast <- DT::renderDataTable(({
#   DT::datatable(blast_combnd, filter='top',
#                 options = list(orderClasses = TRUE, autoWidth=T))
# }))
#
# DT::dataTableOutput("blast", height=1000, width=800)

```