Input HPO quality control
HPO terms with IC values less than 1 are marked in red, and they do not give much information to our system. Please, if possible, select more specific HPO terms suggested in Possible child HPO terms column.
<%= table(id: :characterised_hpos, header: true, border: 2,
cell_align: %w(left center center center center left)) do |data|
data.each do |row|
row.each_with_index do |cell, i|
if i == 1
# STDERR.puts cell.inspect
row[i] = get_hpo_link(cell)
elsif i == 4
row[i] = cell.map{|h,n| [get_hpo_link(h), n].compact}.join(', ')
elsif i == 5
row[i] = cell.map{|r| "#{get_hpo_link(r.first)} (#{r.last})"}.join(', ')
elsif i == 3
ci = cell.to_f
if ci <= 1
text = red_text(ci.round(2))
else
text = ci.round(2)
end
row[i] = text
elsif i == 2
if cell == 'no'
row[i] = red_text(cell)
end
end
end
end
data.unshift([add_tip("HPO name", "Name of the HPO"), "HPO code", "Exists in database?", "Information Coefficient (IC)", "Is child of", "Possible child HPO terms"])
end
%>
Regions associated to HPO profile
General representation
<%=
if !@hash_vars[:merged_regions].nil?
circular_data = []
@hash_vars[:merged_regions].sort{|reg1, reg2| [reg1[0].to_i, reg1[1].to_i] <=> [reg2[0].to_i, reg2[1].to_i]}.each do |row|
#TODO if chr were x or y, change them to 23 and 24 and, when print, use x and y again
circular_data_row = []
circular_data_row << "#{row[1]}-#{row[2]}"
circular_data_row << row[5]
circular_data_row << row[0]
circular_data << circular_data_row
end
circular_data.unshift(%w[Coords CombScore Chr])
@hash_vars[:circular_data] = circular_data
circular(
id: :circular_data,
header: true,
row_names: true,
responsive: false,
sample_attributes: {'Chr' => 2},
config:{
# 'smpLabelOrientation' => 'circular',
'smpOverlays' => ['Chr'],
'colorSpectrum' => ["#d73027", "#fc8d59", "#fee090", "#ffffbf", "#e0f3f8", "#91bfdb", "#4575b4"],
# 'segregateSamplesBy' => ['Chr']
}
) do |data|
data.pop #Discard chromosome data
end
end
%>
Ranked genomic regions associated to the HPO profile
The following table shows all the predicted genomic regions, the HPO terms found for it, their original association values and the calculated combined score. Results are ranked from the highest to the lowest combined score.
<%=
if !@hash_vars[:merged_regions].nil?
gene_var = @hash_vars[:genes_with_kegg_data]
table(id: :merged_regions, header: true, border: 2,
cell_align: %w(center center center left center center)) do |data|
hpo_metadata = @hash_vars[:hpo_metadata]
data.each_with_index do |row, row_number|
row.each_with_index do |cell, i|
if i == 3
row[i] = cell.map{|h| "#{get_hpo_link(h)}: #{hpo_metadata[h][1]}"}.join("\n
")
elsif i == 4
row[i] = cell.map{|a|
if a.abs > 0.01
a.to_f.round(2)
else
"%e" %a
end
}.join("\n
")
end
end
if !gene_var.nil?
gene_data = gene_var[row_number]
if !gene_data.empty?
table = '
'
table << "| #{["GeneID", "Gene Names", "Description", "KEGG pathways"].join(' | ')} |
|---|
"
geneIDs = gene_data.map{|gd| gd.first}
gene_data.each do |geneID, attributes|
table << ''
table << "| #{geneID} | "
if !attributes.nil?
table << "#{attributes[0][0..1].join(', ')} | "
table << "#{attributes[1]} | "
table << "#{attributes[2].map{|pws| "#{pws.last}"}.join('
')} | "
else
table << ' | ' * 3
end
table << '
'
end
table << '
'
row << table
else
row << ('-')
end
else
row << ('-')
end
end
data.unshift(["Chromosome", "Start", "Stop", "Associated HPOs", "Association values
(For each HPO)", "Combined score", "Gene data" ])
end
end
%>
<% if !@hash_vars[:pathway_stats].empty? %>
KEGG pathways significance in the genes located into the predicted regions
<%= table(id: :pathway_stats, header: true, border: 2 ) do |data|
data.each do |row|
row.each_with_index do |field, i|
new_field = field
if i == 0
new_field = "
#{field.last}"
elsif i == 1
new_field = field.map{|geneID| "
#{geneID}" }.join(', ')
elsif i == 2
new_field = field.join(", ")
end
row[i] = new_field
end
end
data.unshift(["KEGG pathway", "Genes in pathway", "Contigency table: PN, NP, PP, NN", "Fisher p-value" ])
end
%>
<% end %>