Class: Report_html

Inherits:
Object
  • Object
show all
Defined in:
lib/report_html/report_html.rb

Instance Method Summary collapse

Constructor Details

#initialize(hash_vars, title = "report", data_from_files = false) ⇒ Report_html

Returns a new instance of Report_html.



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# File 'lib/report_html/report_html.rb', line 9

def initialize(hash_vars, title = "report", data_from_files = false)
	@all_report = ""
	@title = title
	@hash_vars = hash_vars
	@data_from_files = data_from_files
	@plots_data = []
	@count_objects = 0
	@dt_tables = [] #Tables to be styled with the DataTables js lib"
	@bs_tables = [] #Tables to be styled with the bootstrap js lib"
end

Instance Method Details

#add_canvas_attr(hash_attr, attr2add) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 509

def add_canvas_attr(hash_attr, attr2add)
	attr2add.each do |attrs|
		attr_name = attrs.shift
		canvas_attr = []
		attrs.each{|at| canvas_attr << "#{attr_name} : #{at}" }
		hash_attr[attr_name] = canvas_attr
	end
end

#add_header_row_names(data, options) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 167

def add_header_row_names(data, options)
	if options[:add_header_row_names] # This check if html object needs a default header/row_names or not
		if !options[:header]
			range = 0..(data.first.length - 1)
			data.unshift(range.to_a)
		end
		if !options[:row_names]
			data.each_with_index do |row, i|
				row.unshift(i) 
			end
		end
	end
end

#add_sample_attributes(data_structure, options) ⇒ Object

CANVASXPRESS METHODS



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# File 'lib/report_html/report_html.rb', line 375

def add_sample_attributes(data_structure, options)
	parsed_sample_attributes = {}
	options[:sample_attributes].each do |key, col|
		data, _, _ = get_data({id: options[:id], fields: [col], text: true})
		data.shift if options[:header]
		parsed_sample_attributes[key] = data.flatten 
	end
	data_structure['x'] = parsed_sample_attributes
end

#assign_rgb(link_data) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 717

def assign_rgb(link_data)
	colors = {
		'red' => [255, 0, 0],
		'green' => [0, 255, 0],
		'black'	=> [0, 0, 0],
		'yellow' => [255, 255, 0],
		'blue' => [0, 0, 255],
		'gray' => [128, 128, 128],
		'orange' => [255, 165, 0],
		'cyan' => [0, 255, 255],
		'magenta' => [255, 0, 255]
	}
	link_data.each do |link|
		code = colors[link[0]]
		if !code.nil?
			link[0] = "rgb(#{code.join(',')})"
		else
			raise "Color link #{link} is not allowed. The allowed color names are: #{colors.keys.join(' ')}"
		end
	end
end

#barplot(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 538

def barplot(user_options = {}, &block)
	default_options = {
		row_names: true
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Bar'
	end
	return html_string
end

#boxplot(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 574

def boxplot(user_options = {}, &block)
	default_options = {
		row_names: true,
		header: true
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Boxplot'
		options[:mod_data_structure] = 'boxplot'
		if options[:extracode].nil?
			options[:extracode] = "C#{object_id}.groupSamples([\"Factor\"]);"
		end
	end
	return html_string
end

#build(template) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 20

def build(template)
	renderered_template = ERB.new(template).result(binding)
	@all_report = "<HTML>\n"
	make_head
	build_body do 
		renderered_template
	end
	@all_report << "\n</HTML>"
end

#build_body ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 30

def build_body
	if !@plots_data.empty?
		@all_report << "<body onload=\"initPage();\">\n#{yield}\n</body>\n"
	else
		@all_report << "<body>\n#{yield}\n</body>\n"
	end
end

#canvasXpress_main(user_options, block = nil) {|options, config, samples, vars, values, object_id, x, z| ... } ⇒ Object

Yields:

  • (options, config, samples, vars, values, object_id, x, z) 


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# File 'lib/report_html/report_html.rb', line 401

def canvasXpress_main(user_options, block = nil)
	# Handle arguments
	#------------------------------------------
	options = {
		id: nil,
		fields: [],
		smp_attr: [],
		var_attr: [],
		segregate: [],
		data_format: 'one_axis',
		responsive: true,
		height: '600px',
		width: '600px',
		header: false,
		row_names: false,
		add_header_row_names: true,
		transpose: true,
		x_label: 'x_axis',
		title: 'Title',
		sample_attributes: {},
		config: {},
		after_render: [],
		treeBy: 's'
	}
	options.merge!(user_options)
	config = {
		'toolbarType' => 'under',
		'xAxisTitle' => options[:x_label],
		'title' => options[:title]
	}
	if  !options[:tree].nil?
		set_tree(options, config)
	end
	config.merge!(options[:config])
	# Data manipulation
	#------------------------------------------
	no_data_string = ERB.new("<div width=\"#{options[:width]}\" height=\"#{options[:height]}\" > <p>NO DATA<p></div>").result(binding)
	data_array, smp_attr, var_attr = get_data(options)
	return no_data_string if data_array.empty?
	block.call(data_array) if !block.nil?
	object_id = "obj_#{@count_objects}_"
	raise("ID #{options[:id]} has not data") if data_array.nil?
	row_length = data_array.first.length
	samples = data_array.shift[1..row_length]
	return no_data_string if data_array.empty?
	vars = []
	data_array.each do |row|
		vars << row.shift
	end
	values = data_array

	x = {}
	z = {}
	add_canvas_attr(x, var_attr) if !var_attr.nil? && !var_attr.empty?
	add_canvas_attr(z, smp_attr) if !smp_attr.nil? && !smp_attr.empty?
	yield(options, config, samples, vars, values, object_id, x, z)
	# Build JSON objects and Javascript code
	#-----------------------------------------------
	@count_objects += 1
	data_structure = {
		'y' => {
			'vars' => vars,
			'smps' => samples,
			'data' => values
		},
		'x' => x,
		'z' => z
	}
	events = false
	info = false
	afterRender = options[:after_render]
	if options[:mod_data_structure] == 'boxplot'
		data_structure['y']['smps'] = nil
		data_structure.merge!({ 'x' => {'Factor' => samples}})
	elsif options[:mod_data_structure] == 'circular'
		data_structure.merge!({ 'z' => {'Ring' => options[:ring_assignation]}})
	end
	add_sample_attributes(data_structure, options) if !options[:sample_attributes].empty?
	extracode = "#{options[:extracode]}\n"
	extracode << segregate_data("C#{object_id}", options[:segregate]) if !options[:segregate].empty?
	extracode << "C#{object_id}.groupSamples(#{options[:group_samples]})\n" if !options[:group_samples].nil?
	plot_data = "
	var data = #{data_structure.to_json};
        var conf = #{config.to_json}; 
       	var events = #{events.to_json};
        var info = #{info.to_json};
        var afterRender = #{afterRender.to_json};                
        var C#{object_id} = new CanvasXpress(\"#{object_id}\", data, conf, events, info, afterRender);\n#{extracode}"
        @plots_data << plot_data
       
        responsive = ''
        responsive = "responsive='true'" if options[:responsive]
	html = "<canvas  id=\"#{object_id}\" width=\"#{options[:width]}\" height=\"#{options[:height]}\" aspectRatio='1:1' #{responsive}></canvas>"
	return ERB.new(html).result(binding)
end

#circular(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 681

def circular(user_options = {}, &block)
	default_options = {
		ring_assignation: [],
		ringsType: [],
		ringsWeight: []
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		options[:mod_data_structure] = 'circular'
		config['graphType'] = 'Circular'
		config['segregateVariablesBy'] = ['Ring']
		if default_options[:ringsType].empty?
			config['ringGraphType'] = Array.new(vars.length, 'heatmap')
		else
			config['ringGraphType'] = default_options[:ringsType]
		end
		if default_options[:ringsWeight].empty?
			size = 100/vars.length
			config['ringGraphWeight'] = Array.new(vars.length, size)
		else
			config['ringGraphWeight'] = default_options[:ringsWeight]
		end
		if default_options[:ring_assignation].empty?
			options[:ring_assignation] = Array.new(vars.length) {|index| (index + 1).to_s}
		else
			options[:ring_assignation] = default_options[:ring_assignation].map{|item| item.to_s}
		end
		if !default_options[:links].nil?
			if !@hash_vars[default_options[:links]].nil? && !@hash_vars[default_options[:links]].empty?
				link_data, _, _ = get_data({id: default_options[:links], fields: [], add_header_row_names: false, text: true, transpose: false}) 
				config['connections'] = assign_rgb(link_data)
			end
		end
	end
	return html_string
end

#circular_genome(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 739

def circular_genome(user_options = {}, &block)
	default_options = {}.merge!(user_options)
	coordinates = user_options[:genomic_coordinates]
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Circular'
		config["arcSegmentsSeparation"] = 3
   	config["colorScheme"] = "Tableau"
   	config["colors"] = ["#332288","#6699CC","#88CCEE","#44AA99","#117733","#999933","#DDCC77","#661100","#CC6677","#AA4466","#882255","#AA4499"]
		config["showIdeogram"] = true
		chr = []
		pos = []
		tags2remove = []
		vars.each_with_index do |var, i|
			coord = coordinates[var]
			if !coord.nil?
				tag = coord.first.gsub(/[^\dXY]/,'')
				if tag == 'X' || tag == 'Y' || (tag.to_i > 0 && tag.to_i <= 22)
					chr << coord.first.gsub(/[^\dXY]/,'')
					pos << coord.last - 1
				else
					tags2remove << i
				end
			else
				tags2remove << i
			end
		end
		tags2remove.reverse_each{|i| ent = vars.delete_at(i); warn("Feature #{ent} has not valid coordinates")} # Remove entities with invalid coordinates
		z['chr'] = chr
		z['pos'] = pos
	end
	return html_string
end

#corplot(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 605

def corplot(user_options = {}, &block) 
	default_options = {
		transpose: false,
		correlationAxis: 'samples'
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Correlation'
		config['correlationAxis'] = default_options[:correlationAxis]
	end
	return html_string
end

#dotplot(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 548

def dotplot(user_options = {}, &block)
	default_options = {
		row_names: true,
		connect: false
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Dotplot'
		if default_options[:connect]
			config['dotplotType'] = "stacked"
			config['connectBy'] = "Connect"
			z[:Connect] = Array.new(vars.length, 1)
		end
	end
	return html_string
end

#embed_img(img_file, img_attribs = nil) ⇒ Object

EMBED FILES



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# File 'lib/report_html/report_html.rb', line 775

def embed_img(img_file, img_attribs = nil)
	img_content = File.open(img_file).read
	img_base64 = Base64.encode64(img_content)
	format = File.basename(img_file).split('.').last
	img_string = "<img #{img_attribs} src=\"data:image/#{format};base64,#{img_base64}\">"
	return img_string
end

#embed_pdf(pdf_file, pdf_attribs = nil) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 783

def embed_pdf(pdf_file, pdf_attribs = nil)
	pdf_content = File.open(pdf_file).read
	pdf_base64 = Base64.encode64(pdf_content)
	pdf_string = "<embed #{pdf_attribs} src=\"data:application/pdf;base64,#{pdf_base64}\" type=\"application/pdf\"></embed>"
	return pdf_string
end

#extract_data(options) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 181

def extract_data(options)
	data = []
	smp_attr = nil
	var_attr = nil
	ids = options[:id]
	fields = options[:fields]
	ids = ids.split(',') if ids.class == String && ids.include?(',') # String syntax
	if ids.class == Array
		fields = fields.split(';').map{|data_fields| data_fields.split(',').map{|fields| fields.to_i} } if fields.class == String # String syntax
		ids.each_with_index do |id, n|
			data_file = extract_fields(id, fields[n])
			if data.empty?
				data.concat(data_file)
			else
				data.each_with_index do |row, n|
					data[n] = row + data_file[n]
				end
			end
		end
	else
		fields = fields.first if fields.class == Array
		smp_attr = process_attributes(extract_fields(ids, options[:smp_attr]), options[:var_attr], aggregated = true) if !options[:smp_attr].nil? && !options[:smp_attr].empty?
		var_attr = process_attributes(extract_rows(ids, options[:var_attr]), options[:smp_attr], aggregated = false) if !options[:var_attr].nil? && !options[:var_attr].empty?
		data = extract_fields(ids, options[:fields], del_fields = options[:smp_attr], del_rows = options[:var_attr])
	end
	return data, smp_attr, var_attr
end

#extract_fields(id, fields, del_fields = [], del_rows = []) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 209

def extract_fields(id, fields, del_fields = [], del_rows = [])
	data = []
	@hash_vars[id].each_with_index do |row, i|
		next if !del_rows.nil? && del_rows.include?(i)
		if fields.empty?
			row = row.dup # Dup generates a array copy that avoids to modify original objects on data manipulation creating graphs
			if !del_fields.nil? 
				del_fields.sort.reverse_each do |j|
					row.delete_at(j)
				end
			end
			data << row
		else
			data << fields.map{|field| row[field]} #Map without bang do the same than dup
		end
	end
	return data
end

#extract_rows(id, rows) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 228

def extract_rows(id, rows)
	table = @hash_vars[id]
	data = rows.map{|field| table[field]}
	return data
end

#get_cell_align(align_vector, position) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 353

def get_cell_align(align_vector, position)
	cell_align = '' 
	if !align_vector.empty? 
		align = align_vector[position]
		cell_align = "align=\"#{align}\""
	end
	return cell_align
end

#get_col_n_row_span(table) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 328

def get_col_n_row_span(table)
	colspan = []
	rowspan = []
	last_row = 0
	table.each_with_index do |row, r|
		rowspan << Array.new(row.length, 1)
		colspan << Array.new(row.length, 1)
		last_col = 0
		row.each_with_index do |col, c|
			if col == 'colspan'
				colspan[r][last_col] += 1
			else
				last_col = c
			end
			if col == 'rowspan'
				rowspan[last_row][c] += 1
			else
				last_row = r
			end
		end
	end
	return rowspan, colspan
end

#get_data(options) ⇒ Object

DATA MANIPULATION METHODS



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# File 'lib/report_html/report_html.rb', line 139

def get_data(options)
	data, smp_attr, var_attr = extract_data(options)
	if !data.empty?
		if @data_from_files # If data on container is loaded using html_report as lib, we don't care about data format
							# if data comes from files and is loaded as strings. We need to format correctly the data.
			rows = data.length
			cols = data.first.length
			if !options[:text]
				rows.times do |r|
					cols.times do |c|
						next if r == 0 && options[:header]
						next if c == 0 && options[:row_names]
						data[r][c] = data[r][c].to_f
					end
				end
			end
		end
		add_header_row_names(data, options)
		if options[:transpose]
			data = data.transpose
			smp_attr_bkp = smp_attr
			smp_attr = var_attr
			var_attr = smp_attr_bkp
		end
	end
	return data, smp_attr, var_attr
end

#get_report ⇒ Object

return all html string



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# File 'lib/report_html/report_html.rb', line 122

def get_report #return all html string
	renderer = ERB.new(@all_report)
	return renderer.result(binding) #binding does accesible all the current ruby enviroment to erb
end

#get_span(colspan, rowspan, row, col) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 315

def get_span(colspan, rowspan, row, col)
	span = []
	colspan_value = colspan[row][col]
	rowspan_value = rowspan[row][col]
	if colspan_value > 1
		span << "colspan=\"#{colspan_value}\""
	end
	if rowspan_value > 1
		span << "rowspan=\"#{rowspan_value}\""
	end
	return span.join(' ')
end

#heatmap(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 564

def heatmap(user_options = {}, &block)
	default_options = {
		row_names: true
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Heatmap'	
	end
	return html_string
end

#line(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 518

def line(user_options = {}, &block)
	default_options = {
		row_names: true			
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Line'	
	end
	return html_string
end

#load_css(css_files) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 47

def load_css(css_files)
	loaded_css = []
	css_files.each do |css_lib|
		loaded_css << File.open(File.join(JS_FOLDER, css_lib)).read
	end
	return loaded_css
end

#load_js_libraries(js_libraries) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 38

def load_js_libraries(js_libraries)
	loaded_libraries = []
	js_libraries.each do |js_lib|
		js_file = File.open(File.join(JS_FOLDER, js_lib)).read
		loaded_libraries << Base64.encode64(js_file)
	end
	return loaded_libraries
end

#make_head ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 55

def make_head
	@all_report << "\t<title>#{@title}</title>
		<head>
			<meta charset=\"utf-8\">
		    <meta http-equiv=\"CACHE-CONTROL\" CONTENT=\"NO-CACHE\">
   			<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />
   			<meta http-equiv=\"Content-Language\" content=\"en-us\" />
   			<meta name=\"viewport\" content=\"width=device-width, initial-scale=1, shrink-to-fit=no\">\n"

   	# ADD JS LIBRARIES AND CSS
	js_libraries = []
	css_files = []
	if !@plots_data.empty?
		js_libraries << 'canvasXpress.min.js'
		css_files << 'canvasXpress.css'
	end

 	if !@dt_tables.empty? || !@bs_tables.empty? #Bootstrap for datatables or only for static tables. Use bootstrap version needed by datatables to avoid incompatibility issues
	 	@all_report << '<link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"/>'+"\n"
	end

	if !@dt_tables.empty? # CDN load, this library is difficult to embed in html file
	 	@all_report << '<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.21/css/dataTables.bootstrap.min.css"/>'+"\n"
		@all_report << '<script type="text/javascript" src="https://code.jquery.com/jquery-3.5.1.js"></script>' + "\n"
		@all_report << '<script type="text/javascript" src="https://cdn.datatables.net/1.10.21/js/jquery.dataTables.min.js"></script>' + "\n"
		@all_report << '<script type="text/javascript" src="https://cdn.datatables.net/1.10.21/js/dataTables.bootstrap.min.js"></script>' + "\n"
 	end	 	

	loaded_js_libraries = load_js_libraries(js_libraries)
	loaded_css = load_css(css_files)
   	loaded_css.each do |css|
		@all_report << "<style type=\"text/css\"/>
				#{css}
			</style>\n"
	end
   	loaded_js_libraries.each do |lib|
		@all_report << "<script src=\"data:application/javascript;base64,#{lib}\" type=\"application/javascript\"></script>\n"
	end
   	
   	# ADD CUSTOM FUNCTIONS TO USE LOADED JS LIBRARIES
   	#canvasXpress objects
   	if !@plots_data.empty?
    	@all_report << "<script>
					var initPage = function () {        
						<% @plots_data.each do |plot_data| %>
							<%= plot_data %>
						<% end %>
					}
				</script>"
	end

   	#DT tables
   	if !@dt_tables.empty?
    	@all_report << "<script>
						<% @dt_tables.each do |dt_table| %>
							$(document).ready(function () {
								$('#<%= dt_table %>').DataTable();
							});
							
						<% end %>
					</script>\n"
	end


	@all_report <<	"</head>\n"
end

#pie(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 589

def pie(user_options = {}, &block) 
	default_options = {
		transpose: false
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Pie'
		if samples.length > 1
			config['showPieGrid'] = true
			config['xAxis'] = samples 
			config['layout'] = "#{(samples.length.to_f/2).ceil}X2" if config['layout'].nil?
			config['showPieSampleLabel'] = true if config['showPieSampleLabel'].nil?
		end
	end
	return html_string
end

#prepare_table_attribs(attribs) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 362

def prepare_table_attribs(attribs)
	attribs_string = ''
	if !attribs.empty?
		attribs.each do |attrib, value|
			attribs_string << "#{attrib}= \"#{value}\" "
		end
	end
	return attribs_string
end

#process_attributes(attribs, delete_items, aggregated = false) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 234

def process_attributes(attribs, delete_items, aggregated = false)
	parsed_attr = []
	if aggregated
		if !delete_items.nil? && !delete_items.empty?
			(1..delete_items.length).reverse_each do |ind|
				attribs.delete_at(1)
			end
		end
		attribs.first.length.times do |i|
			parsed_attr << attribs.map{|at| at[i]}
		end
	else
		attribs.each do |attrib|
			if !delete_items.nil? && !delete_items.empty?
				(1..delete_items.length).reverse_each do |ind|
					attrib.delete_at(ind)
				end
			end
			parsed_attr << attrib
		end			
	end
	return parsed_attr
end

#scatterbubble2D(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 640

def scatterbubble2D(user_options = {}, &block)
	default_options = {
		row_names: true,
		transpose: false
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'ScatterBubble2D'
		if options[:xAxis].nil?	
			config['xAxis'] = [samples[0]]
		else
			config['xAxis'] = options[:xAxis]
		end
		if options[:yAxis].nil?	
			config['yAxis'] = [samples[1]]
		else
			config['yAxis'] = options[:yAxis]
		end
		if options[:zAxis].nil?	
			config['zAxis'] = [samples[2]]
		else
			config['zAxis'] = options[:zAxis]
		end
		if default_options[:y_label].nil?
			config['yAxisTitle'] = 'y_axis'
		else
			config['yAxisTitle'] = default_options[:y_label]
		end
		if default_options[:z_label].nil?
			config['zAxisTitle'] = 'z_axis'
		else
			config['zAxisTitle'] = default_options[:z_label]
		end
		if !options[:upper_limit].nil? && !options[:lower_limit].nil? && !options[:ranges].nil?
			diff = (options[:upper_limit] - options[:lower_limit]).to_f/options[:ranges]
			sizes = Array.new(options[:ranges]) {|index| options[:lower_limit] + index * diff}
			config['sizes'] = sizes
		end
	end
	return html_string
end

#sccater2D(user_options = {}, &block) ⇒ Object Also known as: scatter2D 



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# File 'lib/report_html/report_html.rb', line 617

def sccater2D(user_options = {}, &block)
	default_options = {
		row_names: false,
		transpose: false
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Scatter2D'
		config['xAxis'] = [samples.first] if config['xAxis'].nil?	
		config['yAxis']	= samples[1..samples.length-1] if config['yAxis'].nil?
		if default_options[:y_label].nil?
			config['yAxisTitle'] = 'y_axis'
		else
			config['yAxisTitle'] = default_options[:y_label]
		end
		if options[:regressionLine]
			options[:extracode] = "C#{object_id}.addRegressionLine();"
		end
	end
	return html_string
end

#segregate_data(obj_id, segregate) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 497

def segregate_data(obj_id, segregate)
	string =""
	segregate.each do |data_type, names|
		if data_type == :var
			string << "#{obj_id}.segregateVariables(#{names.inspect});\n"
		elsif data_type == :smp
			string << "#{obj_id}.segregateSamples(#{names.inspect});\n"
		end
	end
	return string
end

#set_tree(options, config) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 390

def set_tree(options, config)
	tree = tree_from_file(options[:tree])
	if options[:treeBy] == 's'
		config['smpDendrogramNewick'] = tree
		config['samplesClustered'] = true
	elsif options[:treeBy] == 'v'
		config['varDendrogramNewick'] = tree
		config['variablesClustered'] = true
	end
end

#stacked(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 528

def stacked(user_options = {}, &block)
	default_options = {
		row_names: true,
	}.merge!(user_options)
	html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
		config['graphType'] = 'Stacked'	
	end
	return html_string
end

#table(user_options = {}, &block) ⇒ Object

TABLE METHODS



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# File 'lib/report_html/report_html.rb', line 259

def table(user_options = {}, &block)
	options = {
		id: nil,
		header: false,
		row_names: false,
		add_header_row_names: false,
		transpose: false,
		fields: [],
		smp_attr: [],
		var_attr: [],			
		border: 1,
		cell_align: [],
		attrib: {}
	}
	options.merge!(user_options)
	table_attr = prepare_table_attribs(options[:attrib])
	array_data, _, _ = get_data(options)
	block.call(array_data) if !block.nil?
	rowspan, colspan = get_col_n_row_span(array_data)
	table_id = 'table_' + @count_objects.to_s
	@dt_tables << table_id if options[:styled] == 'dt'
	@bs_tables << table_id if options[:styled] == 'bs'
	tbody_tag = false
	html = "
	<table id=\"#{table_id}\" border=\"#{options[:border]}\" #{table_attr}>
		<% if options[:header] %>
			<thead>
		<% end %>
		<% array_data.each_with_index do |row, i| %>
			<% if options[:header] && i == 1 %>
				<tbody>
			<% end %>
			<tr>
				<% row.each_with_index do |cell, j|
					if cell != 'colspan' && cell != 'rowspan' 
						if i == 0 && options[:header] %>
							<th <%= get_span(colspan, rowspan, i, j) %>><%= cell %></th>
						<% else %>
							<td <%= get_cell_align(options[:cell_align], j) %> <%= get_span(colspan, rowspan, i, j) %>><%= cell %></td>
						<% end 
					end %>
				<% end %>
			</tr>
			<% if i == 0 && options[:header] %>
				</thead>
			<% end %>
		<% end %>
		<% if options[:header] %>
			</tbody>
		<% end %>
	</table>
	"
	@count_objects += 1  
	return ERB.new(html).result(binding)
end

#tree_from_file(file) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 385

def tree_from_file(file)
        string_tree = File.open(file).read.gsub("\n", '')
        return string_tree
end

#write(file) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 127

def write(file)
	#dir = File.dirname(file)
	string_report = get_report
	#FileUtils.cp_r(JS_FOLDER, dir) 
	File.open(file, 'w'){|f| f.puts string_report}
end