report_html 0.4.1 → 0.5.6

data/lib/report_html/report_html.rb

@@ -137,8 +137,7 @@ class Report_html
 	# DATA MANIPULATION METHODS
 	#-------------------------------------------------------------------------------------	
 	def get_data(options)
-		data = []
-		data = extract_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.
@@ -155,9 +154,14 @@ class Report_html
 				end
 			end
 			add_header_row_names(data, options)
-			data = data.transpose if options[:transpose]
+			if options[:transpose]
+				data = data.transpose
+				smp_attr_bkp = smp_attr
+				smp_attr = var_attr
+				var_attr = smp_attr_bkp
+			end
 		end
-		return data
+		return data, smp_attr, var_attr
 	end
 
 	def add_header_row_names(data, options)
@@ -176,6 +180,8 @@ class Report_html
 
 	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
@@ -193,16 +199,25 @@ class Report_html
 			end
 		else
 			fields = fields.first if fields.class == Array
-			data = extract_fields(ids, options[:fields])
+			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
+		return data, smp_attr, var_attr
 	end
 
-	def extract_fields(id, fields)
+	def extract_fields(id, fields, del_fields = [], del_rows = [])
 		data = []
-		@hash_vars[id].each do |row|
+		@hash_vars[id].each_with_index do |row, i|
+			next if !del_rows.nil? && del_rows.include?(i)
 			if fields.empty?
-				data << row.dup # Dup generates a array copy that avoids to modify original objects on data manipulation creating graphs
+				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
@@ -210,6 +225,35 @@ class Report_html
 		return data
 	end
 
+	def extract_rows(id, rows)
+		table = @hash_vars[id]
+		data = rows.map{|field| table[field]}
+		return data
+	end
+
+	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
 	# TABLE METHODS
 	#-------------------------------------------------------------------------------------
 	def table(user_options = {}, &block)
@@ -220,13 +264,15 @@ class Report_html
 			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)
+		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
@@ -329,7 +375,7 @@ class Report_html
 	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, _, _ = get_data({id: options[:id], fields: [col], text: true})
 			data.shift if options[:header]
 			parsed_sample_attributes[key] = data.flatten 
 		end
@@ -358,6 +404,9 @@ class Report_html
 		options = {
 			id: nil,
 			fields: [],
+			smp_attr: [],
+			var_attr: [],
+			segregate: [],
 			data_format: 'one_axis',
 			responsive: true,
 			height: '600px',
@@ -386,7 +435,7 @@ class Report_html
 		# Data manipulation
 		#------------------------------------------
 		no_data_string = ERB.new("<div width=\"#{options[:width]}\" height=\"#{options[:height]}\" > <p>NO DATA<p></div>").result(binding)
-		data_array = get_data(options)
+		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}_"
@@ -400,7 +449,11 @@ class Report_html
 		end
 		values = data_array
 
-		yield(options, config, samples, vars, values, object_id)
+		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
@@ -409,7 +462,9 @@ class Report_html
 				'vars' => vars,
 				'smps' => samples,
 				'data' => values
-			}
+			},
+			'x' => x,
+			'z' => z
 		}
 		events = false
 		info = false
@@ -422,6 +477,7 @@ class Report_html
 		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};
@@ -438,11 +494,32 @@ class Report_html
 		return ERB.new(html).result(binding)
 	end
 
+	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
+
+	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
+
 	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|
+		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
 			config['graphType'] = 'Line'	
 		end
 		return html_string
@@ -452,7 +529,7 @@ class Report_html
 		default_options = {
 			row_names: true,
 		}.merge!(user_options)
-		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
+		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
 			config['graphType'] = 'Stacked'	
 		end
 		return html_string
@@ -462,17 +539,33 @@ class Report_html
 		default_options = {
 			row_names: true
 		}.merge!(user_options)
-		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
+		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
 
+	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
+
 	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|
+		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id, x, z|
 			config['graphType'] = 'Heatmap'	
 		end
 		return html_string
@@ -483,7 +576,7 @@ class Report_html
 			row_names: true,
 			header: true
 		}.merge!(user_options)
-		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
+		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?
@@ -497,7 +590,7 @@ class Report_html
 		default_options = {
 			transpose: false
 		}.merge!(user_options)
-		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
+		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
@@ -509,12 +602,24 @@ class Report_html
 		return html_string
 	end
 
+	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
+
 	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|
+		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?
@@ -537,7 +642,7 @@ class Report_html
 			row_names: true,
 			transpose: false
 		}.merge!(user_options)
-		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
+		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]]
@@ -579,7 +684,7 @@ class Report_html
 			ringsType: [],
 			ringsWeight: []
 		}.merge!(user_options)
-		html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
+		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']
@@ -601,7 +706,7 @@ class Report_html
 			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}) 
+					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
@@ -631,6 +736,39 @@ class Report_html
 		end
 	end
 
+	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	
+
 	# EMBED FILES
 	###################################################################################
 

data/lib/report_html/version.rb

@@ -1,3 +1,3 @@
 module ReportHtml
-  VERSION = "0.4.1"
+  VERSION = "0.5.6"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: report_html
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.5.6
 platform: ruby
 authors:
 - seoanezonjic
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-09-01 00:00:00.000000000 Z
+date: 2022-03-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -62,9 +62,7 @@ files:
 - bin/report_html
 - bin/setup
 - js/canvasXpress.css
-- js/canvasXpress.css_old
 - js/canvasXpress.min.js
-- js/canvasXpress.min.js_old
 - js/canvasXpress_license
 - lib/report_html.rb
 - lib/report_html/report_html.rb
@@ -74,7 +72,7 @@ homepage: ''
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -89,9 +87,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.14
-signing_key: 
+rubygems_version: 3.2.15
+signing_key:
 specification_version: 4
 summary: Gem to build html interactive reports.
 test_files: []