report_html 0.3.8 → 0.4.6

data/lib/report_html/report_html.rb

@@ -14,6 +14,7 @@ class Report_html
 		@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
 
 	def build(template)
@@ -57,7 +58,8 @@ class Report_html
 				<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\" />\n"
+    			<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 = []
@@ -66,10 +68,18 @@ class Report_html
 			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/v/dt/jq-3.3.1/dt-1.10.21/datatables.min.css"/>'+"\n"
-	 		@all_report << '<script type="text/javascript" src="https://cdn.datatables.net/v/dt/jq-3.3.1/dt-1.10.21/datatables.min.js"></script>'+"\n"
-	 	end
+		 	@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|
@@ -221,6 +231,7 @@ class Report_html
 		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}>
@@ -364,7 +375,7 @@ class Report_html
 		}
 		options.merge!(user_options)
 		config = {
-			'toolbarPermanent' => true,
+			'toolbarType' => 'under',
 			'xAxisTitle' => options[:x_label],
 			'title' => options[:title]
 		}
@@ -389,7 +400,9 @@ class Report_html
 		end
 		values = data_array
 
-		yield(options, config, samples, vars, values, object_id)
+		x = {}
+		z = {}
+		yield(options, config, samples, vars, values, object_id, x, z)
 		# Build JSON objects and Javascript code
 		#-----------------------------------------------
 		@count_objects += 1
@@ -398,7 +411,9 @@ class Report_html
 				'vars' => vars,
 				'smps' => samples,
 				'data' => values
-			}
+			},
+			'x' => x,
+			'z' => z
 		}
 		events = false
 		info = false
@@ -431,7 +446,7 @@ 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'] = 'Line'	
 		end
 		return html_string
@@ -441,7 +456,7 @@ 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
@@ -451,17 +466,33 @@ 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
@@ -472,7 +503,7 @@ 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?
@@ -486,7 +517,7 @@ 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
@@ -498,12 +529,24 @@ 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?
@@ -519,12 +562,14 @@ class Report_html
 		return html_string
 	end
 
+	alias scatter2D sccater2D # Fix for wrong name method 
+
 	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|
+		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]]
@@ -566,7 +611,7 @@ 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']
@@ -618,6 +663,39 @@ 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 = "0.3.8"
+  VERSION = "0.4.6"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: report_html
 version: !ruby/object:Gem::Version
-  version: 0.3.8
+  version: 0.4.6
 platform: ruby
 authors:
 - seoanezonjic
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-06-02 00:00:00.000000000 Z
+date: 2021-12-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -72,7 +72,7 @@ homepage: ''
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -87,9 +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: []