User-defined default expansion of sections. Fixes #19.

.gitignore

@@ -21,3 +21,4 @@ build.sh
 
 .DS_Store
 de.walware.r.core.prefs
+*.sublime-*

Nozzle.R1/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Nozzle.R1
 Type: Package
 Title: Nozzle Reports
-Version: 1.3-0
-Date: 2012-06-23
+Version: 1.4-0
+Date: 2014-07-25
 Author: Nils Gehlenborg <nils@hms.harvard.edu>
 Maintainer: Nils Gehlenborg <nils@hms.harvard.edu>
 Description: The Nozzle package provides an API to generate HTML reports with

Nozzle.R1/NEWS

@@ -1,3 +1,10 @@
+Release R1-1.4-0 / 25 June 2014
+
+- User-defined default expansion for sections and subsections is now supported
+  by the newSection() and newSubSection() parameter 'expanded'. 
+
+-----------------
+
 Release R1-1.3-0 / 23 June 2013
 
 - Added support to add and display of "related reports", e.g. the reports that

Nozzle.R1/R/nozzle.R

@@ -4,7 +4,7 @@
 # Harvard Medical School, Center for Biomedical Informatics
 # Broad Institute, Cancer Program
 #
-# Copyright (c) 2011-2013. All rights reserved.
+# Copyright (c) 2011-2014. All rights reserved.
 #
 # TODO: add default state (open/closed) for sections (per default all will be closed in custom reports)
 
@@ -14,8 +14,8 @@
 #' \tabular{ll}{
 #' Package: \tab Nozzle.R1\cr
 #' Type: \tab Package\cr
-#' Version: \tab 1.3-0\cr
-#' Date: \tab 2013-06-23\cr
+#' Version: \tab 1.4-0\cr
+#' Date: \tab 2014-07-25\cr
 #' License: \tab LGPL (>= 2)\cr
 #' LazyLoad: \tab yes\cr
 #' }
@@ -708,16 +708,16 @@ newReport <- function( ..., version=0 )
 		element <- .newGeneralReport( "Nozzle Report", version=version );
 	}
 
-	overview <- newSection( "Overview" );
+	overview <- newSection( "Overview", expanded=TRUE );
 	overview$domId <- "overview";
 
 	introduction <- newSubSection( "Introduction" );
 	introduction$domId <- "introduction";
 
-	summary <- newSubSection( "Summary" );
+	summary <- newSubSection( "Summary", expanded=TRUE );
 	summary$domId  <- "summary";
 
-	results <- newSection( "Results", class="results" );
+	results <- newSection( "Results", class="results", expanded=TRUE );
 	results$domId  <- "results";
 
 	methods <- newSection( "Methods & Data" );
@@ -2492,12 +2492,17 @@ addToMeta <- function( report, ... )
 #' @param class If set to SECTION.CLASS.RESULTS, results can be reported in this section. If set to SECTION.CLASS.META the section will be a meta data section. 
 #' @param exportId Unique string to identify this element. Used to retrieve the element using \code{getExportedElement}. 
 #' @param protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PROTECTION.PRIVATE.
+#' @param expanded Whether the section should expanded by default or not. 
 #' @export
 #' @return New element.
 #' 
 #' @author Nils Gehlenborg \email{nils@@hms.harvard.edu}
-newSection <- function( ..., class="", exportId=NULL, protection=PROTECTION.PUBLIC )
+newSection <- function( ..., class="", exportId=NULL, protection=PROTECTION.PUBLIC, expanded=FALSE )
 {
+	if ( expanded ) {
+		class <- .concat( class, " visible" );
+	}
+
 	return ( .newElement( .ELEMENT.SECTION, .concat( ... ), class=class, exportId=exportId, protection=protection ) );
 }
 
@@ -2506,13 +2511,20 @@ newSection <- function( ..., class="", exportId=NULL, protection=PROTECTION.PUBL
 #' @param ... Strings that will be concatenated to form the subsection title. 
 #' @param exportId Unique string to identify this element. Used to retrieve the element using \code{getExportedElement}. 
 #' @param protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PROTECTION.PRIVATE.
+#' @param expanded Whether the section should expanded by default or not. This will not affect the state of parent sections.
 #' @export
 #' @return New element.
 #' 
 #' @author Nils Gehlenborg \email{nils@@hms.harvard.edu}
-newSubSection <- function( ..., exportId=NULL, protection=PROTECTION.PUBLIC )
+newSubSection <- function( ..., exportId=NULL, protection=PROTECTION.PUBLIC, expanded=FALSE )
 {
-	return ( .newElement( .ELEMENT.SUBSECTION, .concat( ... ), exportId=exportId, protection=protection ) );
+	class <- "";
+
+	if ( expanded ) {
+		class <- "visible";
+	}
+
+	return ( .newElement( .ELEMENT.SUBSECTION, .concat( ... ), class=class, exportId=exportId, protection=protection ) );
 }
 
 

Nozzle.R1/inst/js/nozzle.js

@@ -1,7 +1,7 @@
 /*
  * Nozzle R Package - JavaScript Library
  *
- * Copyright 2011-2013, Harvard Medical School / Broad Institute
+ * Copyright 2011-2014, Harvard Medical School / Broad Institute
  * Authored and maintained by Nils Gehlenborg (nils@hms.harvard.edu)
  */
 
@@ -201,7 +201,8 @@ function applyFilePrefixPostfix( prefix, postfix )
 	ToggleMode = {
 	    TOGGLE: 0,
 	    SHOW: 1,
-	    HIDE: 2
+	    HIDE: 2,
+	    INITIALIZE: 3
 	};	
 
 	var toggleContents = function( section, animation, mode, target )
@@ -227,6 +228,25 @@ function applyFilePrefixPostfix( prefix, postfix )
 
 			switch ( mode )
 			{
+				case ToggleMode.INITIALIZE:
+					if ( section.hasClass( "visible" ) )
+					{
+						console.log( "Showing section ", section );
+						body.show();
+						if ( summarySignificant !== undefined )
+						{
+							summarySignificant.addClass( "deactivated" );
+						}					
+					}
+
+					if ( !section.hasClass( "visible" ) )
+					{
+						body.hide();
+					}
+
+					button.text( section.hasClass( "visible" ) ? "-" : "+" );					
+					button.attr( "title", section.hasClass( "visible" ) ? "Click to collapse" : "Click to expand" );					
+					break;
 				case ToggleMode.TOGGLE:
 					if ( subSections.length == 1 )
 					{
@@ -291,7 +311,6 @@ function applyFilePrefixPostfix( prefix, postfix )
 		var sectionheaders = $( "#" + reportId + " .sectionheader" ).not( ".evidence .sectionheader, .subsubsection .sectionheader" );
 
 		sectionheaders.prepend( "<span class=\"button contenttoggle\"><a>" + "-" + "</a></span>" );
-		sectionheaders.parent().addClass( "visible" );
 
 		var buttons = $( "#" + reportId + " .button.contenttoggle" );
 
@@ -826,9 +845,9 @@ function reloadStylesheets() {
 	} );
 
 	var toggleDefaultState = function( animate )	{	
-		toggleAllContents( animate, ToggleMode.HIDE );	   			
-		toggleContents( $( "#overview_" + reportId + ", #summary_" + reportId ), animate );				
-		toggleContents( $( "#results_" + reportId ), animate );				
+		toggleAllContents( animate, ToggleMode.INITIALIZE );
+		//toggleContents( $( "#overview_" + reportId + ", #summary_" + reportId ), animate );				
+		//toggleContents( $( "#results_" + reportId ), animate );
 	};
 
 	toggleDefaultState( false );

Nozzle.R1/man/Nozzle.R1-package.Rd

@@ -9,8 +9,8 @@
 }
 \details{
   \tabular{ll}{ Package: \tab Nozzle.R1\cr Type: \tab
-  Package\cr Version: \tab 1.3-0\cr Date: \tab
-  2013-06-23\cr License: \tab LGPL (>= 2)\cr LazyLoad: \tab
+  Package\cr Version: \tab 1.4-0\cr Date: \tab
+  2014-07-24\cr License: \tab LGPL (>= 2)\cr LazyLoad: \tab
   yes\cr }
 
   Nozzle was designed to facilitate summarization and rapid

Nozzle.R1/man/newSection.Rd

@@ -3,7 +3,7 @@
 \title{Create a new section element.}
 \usage{
   newSection(..., class = "", exportId = NULL,
-    protection = PROTECTION.PUBLIC)
+    protection = PROTECTION.PUBLIC, expanded = FALSE)
 }
 \arguments{
   \item{...}{Strings that will be concatenated to form the
@@ -19,6 +19,9 @@
 
   \item{protection}{Procection level. One of
   PROTECTION.PUBLIC, PROTECTION.GROUP, PROTECTION.PRIVATE.}
+
+  \item{expanded}{Whether the section should expanded by
+  default or not.}
 }
 \value{
   New element.

Nozzle.R1/man/newSubSection.Rd

@@ -3,7 +3,7 @@
 \title{Create a new subsection element.}
 \usage{
   newSubSection(..., exportId = NULL,
-    protection = PROTECTION.PUBLIC)
+    protection = PROTECTION.PUBLIC, expanded = FALSE)
 }
 \arguments{
   \item{...}{Strings that will be concatenated to form the
@@ -15,6 +15,10 @@
 
   \item{protection}{Procection level. One of
   PROTECTION.PUBLIC, PROTECTION.GROUP, PROTECTION.PRIVATE.}
+
+  \item{expanded}{Whether the section should expanded by
+  default or not. This will not affect the state of parent
+  sections.}
 }
 \value{
   New element.

examples/demo.R

@@ -318,10 +318,10 @@ report2 <- setPreviousReport( report2, "nozzle1.html", "Demo 1" );
 report2 <- addTo( report2, addTo( newSection( "My Introduction" ), newParagraph( "Hello World! This is a paragraph of text!" ) ) );
 report2 <- addTo( report2, addTo( newSection( "My Methods" ), method2 ) );
 
-report2 <- addTo( report2, addTo( newSection( "My Results", class="results" ),
+report2 <- addTo( report2, addTo( newSection( "My Results", class="results", expanded=TRUE ),
 				addTo( newSubSection( "Nozzle Figure" ), figure1, figure2 ),
 				addTo( newSubSection( "Nozzle Table" ), table1, table4, table3, table5 ), 
-				addTo( newSubSection( "Nozzle Text" ), paragraph1, list, paragraph2, paragraphPublic,
+				addTo( newSubSection( "Nozzle Text", expanded=TRUE ), paragraph1, list, paragraph2, paragraphPublic,
 							paragraphGroup, paragraphPrivate ),
 				addTo( addTo( newSubSection( "Nozzle Results" ), newParagraph( "A result: ", asSummary( result4 ), ", yay!" ) ) ) ) ); 
 
@@ -367,7 +367,7 @@ writeReport( report1, filename="reports/nozzle1_private", level=PROTECTION.PRIVA
 
 # Examples for Developers
 # write a "debug" development version that uses external JS or external CSS for rapid development
-#writeReport( report1, filename="reports/nozzle1_debug", debug=TRUE, level=PROTECTION.PRIVATE,
+# writeReport( report1, filename="reports/nozzle1_debug", debug=TRUE, level=PROTECTION.PRIVATE,
 #	debugJavaScript="/Users/nils/Projects/Nozzle/Nozzle.R1/inst/js/nozzle.js",
 #	debugCss="/Users/nils/Projects/Nozzle/Nozzle.R1/inst/css/nozzle.css" );