msa.qmd

---
title: "Alignments"
---

```{r}
# Prepare data for filtering
library(tidyverse)

redundant <-
  'data/L_redundant.tsv' |>
  read_tsv() |>
  select(motif = redundant) |>
  unique()

motif <-
  'data/potentially-novel-motifs.tsv' |>
  read_tsv() |>
  anti_join(redundant, 'motif')

motif %>%
  mutate_at('motif', str_remove, '\\.fna\\.motif') |>
  pull(motif) %>%
  unique %>%
  sort -> motifs_list

ojs_define(motifs_list = motifs_list)
```

::: {style="display: none;"}
```{ojs}
//Check GET variable `candidate` for what motif to choose, otherwise default to first one
para = window.location.href.match(/(?<=candidate=)(.*?)[^&]+/)
sv = {
  if ( para !== null ) {
    if ( motifs_list.includes(para[0]) ) {
      return para[0]
    }
  }
  return motifs_list[0] 
}
```
:::

```{ojs}
infoHelper = function(x, lab, txt) {
  // The element to show
  let res = html`${lab} <span class='myInfo' id='${x}'>ⓘ</span>`
  // Add tippy tooltip
  // Iusse: add with delay, otherwise the span was not yet displayed
  setTimeout(function() {
    tippy('#' + x, {
      content: txt 
    })
  }, 500)
  return(res)
}

// Choose a single motif
viewof sel = Inputs.select(
  motifs_list,
  {
    label: 'Alignment for',
    value: sv
  }
)

html`Download alignment as <a href="https://rth.dk/resources/crs/cyanobacteria/data/motifs/${sel}.sto">Stockholm</a> | <a href="https://rth.dk/resources/crs/cyanobacteria/data/motifs-fasta/${sel}.fasta">Fasta</a> | <a href="https://rth.dk/resources/crs/cyanobacteria/data/jalview/${sel}.svg">Figure</a>`

html`<a href="https://rth.dk/resources/crs/cyanobacteria/candidate.html?candidate=${sel}">View CRS details</a>`
```

```{ojs}
html`<center><img src="https://rth.dk/resources/crs/cyanobacteria/data/jalview/${sel}.svg" class = 'jalview'/></center>`
```

Visualization made with [Jalview](https://www.jalview.org/).