Browse CRSs

Filter selection

data = transpose(motifs)
data_path = transpose(motifs_paths)

taxes_tbl = transpose(taxes)
motif_taxes_tbl = transpose(motif_taxes)

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)
}


// Build the filtering form
viewof filters = Inputs.form({
  cat: Inputs.checkbox(
    categories,
    {
      label: infoHelper(
        'infoCat',
        'Category',
        'Depending on R-scape assessed alignment power and covariation for cutoff 20%'
      ),
      // check all per default
      value: categories
    }
  ),
  side: Inputs.radio(
    ['either', 'upstream', 'downstream'],
    {
      label: infoHelper(
        'infoLoc',
        'Relative position',
        'Location relative to the ortholog anchor'
      ),
      value: 'either'
    }
  ),
  searchregion: Inputs.toggle({
    label: infoHelper(
      'infoReg',
      'No known structure',
      'Select to only include candidates detected in intergenic search regions that do not overlap any known structures in any genome'
    ),
    value: false
  }),
  pathway: Inputs.select(
    pathways,
    {
      sort: true,
      label: infoHelper(
        'infoPath',
        'Pathway',
        'Filter by pathway association of the gene ortholog adjacent to which candidates were detected'
      )
    }
  ),
  transcribed: Inputs.toggle({
    label: infoHelper(
      'infoTrans',
      'Transcribed',
      'Select if candidate should be detected as transcriptionally active in at least one genome'
    ),
    value: false
  }),
})

viewof tax_search = Inputs.search(taxes_tbl, {
  label: infoHelper(
    'infoPhylo',
    'Phylogeny',
    'Filter per NCBI taxonmy annotated phylogeny'
  ),
  columns: ["order", "family", "genus", "species"]
})
viewof tax = Inputs.table(tax_search, {
  columns: ["order", "family", "genus", "species"]
  // select all per default
  //value: tax_search.keys()
})

// number of motifs selected vs total
no_tax_filtered = Array.from(tax).length
no_tax_total = Array.from(taxes_tbl).length

• You can filter either via the search box or select individual species with the checkbox to the left of each row
• The current phylogenetic filtering is set to of species.

path_filtered = data_path.filter(function(row) {
  return row.pathway === filters.pathway
})
path_motifs = path_filtered.map(x => x.motif)

// Extract from phylogeny which taxrow to keep, then match to motifs to keep
tax_filtering = tax.map(x => x.taxrow)
tax_motif_filtering = motif_taxes_tbl.
  filter(row => tax_filtering.includes(row.taxrow)).
  map(x => x.motif)

filtered = data.filter(function(row) {
  // check all negative cases in which rows should be filtered out
  if ( ! filters.cat.includes(row.Category) ) {
    // not in a selected category
    return false
  }
  if ( filters.side !== 'either' ) {
    if ( row.Side !== filters.side) {
      // not the selected side
      return false
    }
  }
  if ( filters.searchregion ) {
    // Filter out motifs that were in search regions in which CMsearch had
    // any hit (even if the motif does not overlap)
    if ( row["Knwon structures in search region"] === 'yes' ) {
      return false
    }
  }
  if ( filters.transcribed ) {
    // Filter for transcriptionally active candidates
    if ( row["Transcribed"] === 0 ) {
      return false
    }
  }
  if ( filters.pathway !== "(no filtering)" ) {
    if ( ! path_motifs.includes(row.Candidate) ) {
      // not in the selected pathway
      return false
    }
  }
  if ( ! tax_motif_filtering.includes(row.Candidate) ) {
    return false
  }
  return true
})


// number of motifs selected vs total
//no_filtered = Array.from(filtered).length
no_filtered = Array.from(filtered_search).length
no_total = Array.from(data).length

Candidates matching filters

Your current filtering criteria matches of predicted RNA structures, that are:

viewof filtered_search = Inputs.search(filtered, {
  label: infoHelper(
    'infoTXT',
    'Ortholog',
    'Full text search orthologs by name'
  ),
  columns: ["Candidate", "Term", "Ortholog"]
})
Inputs.table(filtered_search, {
  columns: [
    "Candidate", "Ortholog",
    "Length", "No. sequences", "No. species",
    "No. base-pairs", // "Paired positions %", 
    //"RNAphylo",
    "FDR (%)",
    'Transcribed',
    //"hmmpair",
    'Average sequence identity (%)',
    "Alignment power (%)", 
    "Covarying bps (%)"
  ],
  format: {
    Candidate: function(i) {
      return html`<a href="candidate.html?candidate=${i}" target="_blank">${i}</a>`
    }
  }
})

• This table is scrollable
• Clicking on the column name in the headers allows sorting the rows by each score
• The columns “Transcribed” referes to the number of genomes in which the candidate was detected to be transcriptionally active