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Add the raw uncompressed .js files needed for rgGRR svg display - the packed ones were already there

Browse Source 
Fix rgManQQ so the manhattan plot is not called for data without chromosome and offset

Use LD reduced data for IBD/GRR for faster performance and better resolution of close relationships
Add an LD pruning and thinning step to rgGRR - the target composite pbed or lped has the thinned files permanently added for reuse.
This is skipped for small numbers of markers since the plink --thin 0.1 option applied to tinywga.pbed will return an empty file
which is not really ideal.
This commit is contained in:
Ross Lazarus
2010-04-13 11:15:35 -04:00
parent 4135f39355
commit 855e2923a2
5 changed files with 2396 additions and 1102 deletions
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static/scripts/checkbox_and_radiobutton.js
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/*
Scripts to create interactive checkboxes and radio buttons in SVG using ECMA script
Copyright (C) <2007> <Andreas Neumann>
Version 1.1.3, 2007-08-09
neumann@karto.baug.ethz.ch
http://www.carto.net/
http://www.carto.net/neumann/
Credits:
* Guy Morton for providing a fix to let users toggle checkboxes by clicking on text labels
* Bruce Rindahl for providing the bugfix described in version 1.1.2
* Simon Shutter for providing a fix for the ASV in IE crash when reloading the SVG file after calling the .remove() method on a checkbox
----
Documentation: http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/
----
current version: 1.1.3
version history:
1.0 (2006-03-13)
initial version
1.1 (2006-07-11)
text labels are now clickable (thanks to Guy Morton)
added method .moveTo() to move checkbox to a different location
introduced new constructor parameter labelYOffset to allow more flexible placement of the text label
1.1.1 (2007-02-06)
added cursor pointer to the text label and use element representing the checkBox
1.1.2 (2007-04-19)
bug fix: this.selectedIndex was not correctly initialized in method addCheckBox of the radioButtonGroup object
1.1.3 (2007-08-09)
bug fix: the method .remove() was slightly modified (using removeEventListener) for avoiding a crash related to the method after reloading the SVG file
-------
This ECMA script library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library (lesser_gpl.txt); if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
----
original document site: http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/
Please contact the author in case you want to use code or ideas commercially.
If you use this code, please include this copyright header, the included full
LGPL 2.1 text and read the terms provided in the LGPL 2.1 license
(http://www.gnu.org/copyleft/lesser.txt)
-------------------------------
Please report bugs and send improvements to neumann@karto.baug.ethz.ch
If you use this control, please link to the original (http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/)
somewhere in the source-code-comment or the "about" of your project and give credits, thanks!
*/
function checkBox(id,parentNode,x,y,checkboxId,checkcrossId,checkedStatus,labelText,textStyles,labelDistance,labelYOffset,radioButtonGroup,functionToCall) {
var nrArguments = 13;
var createCheckbox= true;
if (arguments.length == nrArguments) {
this.id = id; //an internal id, this id is not used in the SVG Dom tree
this.parentNode = parentNode; //the parentNode, string or nodeReference
this.x = x; //the center of the checkBox
this.y = y; //the center of the checkBox
this.checkboxId = checkboxId; //the id of the checkbox symbol (background)
this.checkcrossId = checkcrossId; //the id of the checkbox symbol (foreground), pointer-events should be set to "none"
this.checkedStatus = checkedStatus; //a status variable (true|false), indicates if checkbox is on or off
this.labelText = labelText; //the text of the checkbox label to be displayed, use undefined or empty string if you don't need a label text
this.textStyles = textStyles; //an array of literals containing the text settings
if (!this.textStyles["font-size"]) {
this.textStyles["font-size"] = 12;
}
this.labelDistance = labelDistance; //a distance defined from the center of the checkbox to the left of the text of the label
this.labelYOffset = labelYOffset; //a y offset value for the text label in relation to the checkbox symbol center
this.radioButtonGroup = radioButtonGroup; //a reference to a radio button group, if this is a standalone checkBox, just use the parameter undefined
this.functionToCall = functionToCall; //the function to call after triggering checkBox
this.exists = true; //status that indicates if checkbox exists or not, is set to false after method .remove() was called
this.label = undefined; //later a reference to the label text node
}
else {
createCheckbox = false;
alert("Error in checkbox ("+id+"): wrong nr of arguments! You have to pass over "+nrArguments+" parameters.");
}
if (createCheckbox) {
//timer stuff
this.timer = new Timer(this); //a Timer instance for calling the functionToCall
if (this.radioButtonGroup) {
this.timerMs = 0;
}
else {
this.timerMs = 200; //a constant of this object that is used in conjunction with the timer - functionToCall is called after 200 ms
}
//create checkbox
this.createCheckBox();
}
else {
alert("Could not create checkbox with id '"+id+"' due to errors in the constructor parameters");
}
}
//this method creates all necessary checkbox geometry
checkBox.prototype.createCheckBox = function() {
if (typeof(this.parentNode) == "string") {
this.parentNode = document.getElementById(this.parentNode);
}
//create checkbox
this.checkBox = document.createElementNS(svgNS,"use");
this.checkBox.setAttributeNS(null,"x",this.x);
this.checkBox.setAttributeNS(null,"y",this.y);
this.checkBox.setAttributeNS(xlinkNS,"href","#"+this.checkboxId);
this.checkBox.addEventListener("click",this,false);
this.checkBox.setAttributeNS(null,"cursor","pointer");
this.parentNode.appendChild(this.checkBox);
//create checkcross
this.checkCross = document.createElementNS(svgNS,"use");
this.checkCross.setAttributeNS(null,"x",this.x);
this.checkCross.setAttributeNS(null,"y",this.y);
this.checkCross.setAttributeNS(xlinkNS,"href","#"+this.checkcrossId);
this.parentNode.appendChild(this.checkCross);
if (this.checkedStatus == false) {
this.checkCross.setAttributeNS(null,"display","none");
}
//create label, if any
if (this.labelText) {
if (this.labelText.length > 0) {
this.label = document.createElementNS(svgNS,"text");
for (var attrib in this.textStyles) {
var value = this.textStyles[attrib];
if (attrib == "font-size") {
value += "px";
}
this.label.setAttributeNS(null,attrib,value);
}
this.label.setAttributeNS(null,"x",(this.x + this.labelDistance));
this.label.setAttributeNS(null,"y",(this.y + this.labelYOffset));
this.label.setAttributeNS(null,"cursor","pointer");
var labelTextNode = document.createTextNode(this.labelText);
this.label.appendChild(labelTextNode);
this.label.setAttributeNS(null,"pointer-events","all");
this.label.addEventListener("click",this,false);
this.parentNode.appendChild(this.label);
}
}
if (this.radioButtonGroup) {
this.radioButtonGroup.addCheckBox(this);
}
}
checkBox.prototype.handleEvent = function(evt) {
if (evt.type == "click") {
if (this.checkedStatus == true) {
this.checkCross.setAttributeNS(null,"display","none");
this.checkedStatus = false;
}
else {
this.checkCross.setAttributeNS(null,"display","inline");
this.checkedStatus = true;
}
}
this.timer.setTimeout("fireFunction",this.timerMs);
}
checkBox.prototype.fireFunction = function() {
if (this.radioButtonGroup) {
this.radioButtonGroup.selectById(this.id,true);
}
else {
if (typeof(this.functionToCall) == "function") {
this.functionToCall(this.id,this.checkedStatus,this.labelText);
}
if (typeof(this.functionToCall) == "object") {
this.functionToCall.checkBoxChanged(this.id,this.checkedStatus,this.labelText);
}
if (typeof(this.functionToCall) == undefined) {
return;
}
}
}
checkBox.prototype.check = function(FireFunction) {
this.checkCross.setAttributeNS(null,"display","inherit");
this.checkedStatus = true;
if (FireFunction) {
this.timer.setTimeout("fireFunction",this.timerMs);
}
}
checkBox.prototype.uncheck = function(FireFunction) {
this.checkCross.setAttributeNS(null,"display","none");
this.checkedStatus = false;
if (FireFunction) {
this.timer.setTimeout("fireFunction",this.timerMs);
}
}
//move checkbox to a different position
checkBox.prototype.moveTo = function(moveX,moveY) {
this.x = moveX;
this.y = moveY;
//move checkbox
this.checkBox.setAttributeNS(null,"x",this.x);
this.checkBox.setAttributeNS(null,"y",this.y);
//move checkcross
this.checkCross.setAttributeNS(null,"x",this.x);
this.checkCross.setAttributeNS(null,"y",this.y);
//move text label
if (this.labelText) {
this.label.setAttributeNS(null,"x",(this.x + this.labelDistance));
this.label.setAttributeNS(null,"y",(this.y + this.labelYOffset));
}
}
checkBox.prototype.remove = function(FireFunction) {
this.checkBox.removeEventListener("click",this,false);
this.parentNode.removeChild(this.checkBox);
this.parentNode.removeChild(this.checkCross);
if (this.label) {
this.parentNode.removeChild(this.label);
}
this.exists = false;
}
checkBox.prototype.setLabelText = function(labelText) {
this.labelText = labelText
if (this.label) {
this.label.firstChild.nodeValue = labelText;
}
else {
if (this.labelText.length > 0) {
this.label = document.createElementNS(svgNS,"text");
for (var attrib in this.textStyles) {
value = this.textStyles[attrib];
if (attrib == "font-size") {
value += "px";
}
this.label.setAttributeNS(null,attrib,value);
}
this.label.setAttributeNS(null,"x",(this.x + this.labelDistance));
this.label.setAttributeNS(null,"y",(this.y + this.textStyles["font-size"] * 0.3));
var labelTextNode = document.createTextNode(this.labelText);
this.label.appendChild(labelTextNode);
this.parentNode.appendChild(this.label);
}
}
}
/* start of the radioButtonGroup object */
function radioButtonGroup(id,functionToCall) {
var nrArguments = 2;
if (arguments.length == nrArguments) {
this.id = id;
if (typeof(functionToCall) == "function" || typeof(functionToCall) == "object" || typeof(functionToCall) == undefined) {
this.functionToCall = functionToCall;
}
else {
alert("Error in radiobutton with ("+id+"): argument functionToCall is not of type 'function', 'object' or undefined!");
}
this.checkBoxes = new Array(); //this array will hold checkbox objects
this.selectedId = undefined; //holds the id of the active radio button
this.selectedIndex = undefined; //holds the index of the active radio button
//timer stuff
this.timer = new Timer(this); //a Timer instance for calling the functionToCall
this.timerMs = 200; //a constant of this object that is used in conjunction with the timer - functionToCall is called after 200 ms
}
else {
alert("Error in radiobutton with ("+id+"): wrong nr of arguments! You have to pass over "+nrArguments+" parameters.");
}
}
radioButtonGroup.prototype.addCheckBox = function(checkBoxObj) {
this.checkBoxes.push(checkBoxObj);
if (checkBoxObj.checkedStatus) {
this.selectedId = checkBoxObj.id;
this.selectedIndex = this.checkBoxes.length - 1;
}
}
//change radio button selection by id
radioButtonGroup.prototype.selectById = function(cbId,fireFunction) {
var found = false;
for (var i=0;i<this.checkBoxes.length;i++) {
if (this.checkBoxes[i].id == cbId) {
this.selectedId = cbId;
this.selectedIndex = i;
if (this.checkBoxes[i].checkedStatus == false) {
this.checkBoxes[i].check(false);
}
found = true;
}
else {
this.checkBoxes[i].uncheck(false);
}
}
if (found) {
if (fireFunction) {
this.timer.setTimeout("fireFunction",this.timerMs);
}
}
else {
alert("Error in radiobutton with ("+this.id+"): could not find checkbox with id '"+cbId+"'");
}
}
//change radio button selection by label name
radioButtonGroup.prototype.selectByLabelname = function(labelName,fireFunction) {
var id = -1;
for (var i=0;i<this.checkBoxes.length;i++) {
if (this.checkBoxes[i].labelText == labelName) {
id = this.checkBoxes[i].id;
}
}
if (id == -1) {
alert("Error in radiobutton with ("+this.id+"): could not find checkbox with label '"+labelName+"'");
}
else {
this.selectById(id,fireFunction);
}
}
radioButtonGroup.prototype.fireFunction = function() {
if (typeof(this.functionToCall) == "function") {
this.functionToCall(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText);
}
if (typeof(this.functionToCall) == "object") {
this.functionToCall.radioButtonChanged(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText);
}
if (typeof(this.functionToCall) == undefined) {
return;
}
}
static/scripts/helper_functions.js
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/**
* @fileoverview
*
* ECMAScript <a href="http://www.carto.net/papers/svg/resources/helper_functions.html">helper functions</a>, main purpose is to serve in SVG mapping or other SVG based web applications
*
* This ECMA script library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library (http://www.carto.net/papers/svg/resources/lesser_gpl.txt); if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
* Please report bugs and send improvements to neumann@karto.baug.ethz.ch
* If you use these scripts, please link to the original (http://www.carto.net/papers/svg/resources/helper_functions.html)
* somewhere in the source-code-comment or the "about" of your project and give credits, thanks!
*
* See <a href="js_docs_out/overview-summary-helper_functions.js.html">documentation</a>.
*
* @author Andreas Neumann a.neumann@carto.net
* @copyright LGPL 2.1 <a href="http://www.gnu.org/copyleft/lesser.txt">Gnu LGPL 2.1</a>
* @credits Bruce Rindahl, numerous people on svgdevelopers@yahoogroups.com
*/
//global variables necessary to create elements in these namespaces, do not delete them!!!!
/**
* This variable is a shortcut to the full URL of the SVG namespace
* @final
* @type String
*/
var svgNS = "http://www.w3.org/2000/svg";
/**
* This variable is a shortcut to the full URL of the XLink namespace
* @final
* @type String
*/
var xlinkNS = "http://www.w3.org/1999/xlink";
/**
* This variable is a shortcut to the full URL of the attrib namespace
* @final
* @type String
*/
var cartoNS = "http://www.carto.net/attrib";
/**
* This variable is a alias to the full URL of the attrib namespace
* @final
* @type String
*/
var attribNS = "http://www.carto.net/attrib";
/**
* This variable is a alias to the full URL of the Batik extension namespace
* @final
* @type String
*/
var batikNS = "http://xml.apache.org/batik/ext";
/**
* Returns the polar direction from a given vector
* @param {Number} xdiff the x-part of the vector
* @param {Number} ydiff the y-part of the vector
* @return direction the direction in radians
* @type Number
* @version 1.0 (2007-04-30)
* @see #toPolarDist
* @see #toRectX
* @see #toRectY
*/
function toPolarDir(xdiff,ydiff) {
var direction = (Math.atan2(ydiff,xdiff));
return(direction);
}
/**
* Returns the polar distance from a given vector
* @param {Number} xdiff the x-part of the vector
* @param {Number} ydiff the y-part of the vector
* @return distance the distance
* @type Number
* @version 1.0 (2007-04-30)
* @see #toPolarDir
* @see #toRectX
* @see #toRectY
*/
function toPolarDist(xdiff,ydiff) {
var distance = Math.sqrt(xdiff * xdiff + ydiff * ydiff);
return(distance);
}
/**
* Returns the x-part of a vector from a given direction and distance
* @param {Number} direction the direction (in radians)
* @param {Number} distance the distance
* @return x the x-part of the vector
* @type Number
* @version 1.0 (2007-04-30)
* @see #toPolarDist
* @see #toPolarDir
* @see #toRectY
*/
function toRectX(direction,distance) {
var x = distance * Math.cos(direction);
return(x);
}
/**
* Returns the y-part of the vector from a given direction and distance
* @param {Number} direction the direction (in radians)
* @param {Number} distance the distance
* @return y the y-part of the vector
* @type Number
* @version 1.0 (2007-04-30)
* @see #toPolarDist
* @see #toPolarDir
* @see #toRectX
*/
function toRectY(direction,distance) {
y = distance * Math.sin(direction);
return(y);
}
/**
* Converts degrees to radians
* @param {Number} deg the degree value
* @return rad the radians value
* @type Number
* @version 1.0 (2007-04-30)
* @see #RadToDeg
*/
function DegToRad(deg) {
return (deg / 180.0 * Math.PI);
}
/**
* Converts radians to degrees
* @param {Number} rad the radians value
* @return deg the degree value
* @type Number
* @version 1.0 (2007-04-30)
* @see #DegToRad
*/
function RadToDeg(rad) {
return (rad / Math.PI * 180.0);
}
/**
* Converts decimal degrees to degrees, minutes, seconds
* @param {Number} dd the decimal degree value
* @return degrees the degree values in the following notation: {deg:degrees,min:minutes,sec:seconds}
* @type literal
* @version 1.0 (2007-04-30)
* @see #dms2dd
*/
function dd2dms(dd) {
var minutes = (Math.abs(dd) - Math.floor(Math.abs(dd))) * 60;
var seconds = (minutes - Math.floor(minutes)) * 60;
var minutes = Math.floor(minutes);
if (dd >= 0) {
var degrees = Math.floor(dd);
}
else {
var degrees = Math.ceil(dd);
}
return {deg:degrees,min:minutes,sec:seconds};
}
/**
* Converts degrees, minutes and seconds to decimal degrees
* @param {Number} deg the degree value
* @param {Number} min the minute value
* @param {Number} sec the second value
* @return deg the decimal degree values
* @type Number
* @version 1.0 (2007-04-30)
* @see #dd2dms
*/
function dms2dd(deg,min,sec) {
if (deg < 0) {
return deg - (min / 60) - (sec / 3600);
}
else {
return deg + (min / 60) + (sec / 3600);
}
}
/**
* log function, missing in the standard Math object
* @param {Number} x the value where the log function should be applied to
* @param {Number} b the base value for the log function
* @return logResult the result of the log function
* @type Number
* @version 1.0 (2007-04-30)
*/
function log(x,b) {
if(b==null) b=Math.E;
return Math.log(x)/Math.log(b);
}
/**
* interpolates a value (e.g. elevation) bilinearly based on the position within a cell with 4 corner values
* @param {Number} za the value at the upper left corner of the cell
* @param {Number} zb the value at the upper right corner of the cell
* @param {Number} zc the value at the lower right corner of the cell
* @param {Number} zd the value at the lower left corner of the cell
* @param {Number} xpos the x position of the point where a new value should be interpolated
* @param {Number} ypos the y position of the point where a new value should be interpolated
* @param {Number} ax the x position of the lower left corner of the cell
* @param {Number} ay the y position of the lower left corner of the cell
* @param {Number} cellsize the size of the cell
* @return interpol_value the result of the bilinear interpolation function
* @type Number
* @version 1.0 (2007-04-30)
*/
function intBilinear(za,zb,zc,zd,xpos,ypos,ax,ay,cellsize) { //bilinear interpolation function
var e = (xpos - ax) / cellsize;
var f = (ypos - ay) / cellsize;
//calculation of weights
var wa = (1 - e) * (1 - f);
var wb = e * (1 - f);
var wc = e * f;
var wd = f * (1 - e);
var interpol_value = wa * zc + wb * zd + wc * za + wd * zb;
return interpol_value;
}
/**
* tests if a given point is left or right of a given line
* @param {Number} pointx the x position of the given point
* @param {Number} pointy the y position of the given point
* @param {Number} linex1 the x position of line's start point
* @param {Number} liney1 the y position of line's start point
* @param {Number} linex2 the x position of line's end point
* @param {Number} liney2 the y position of line's end point
* @return leftof the result of the leftOfTest, 1 means leftOf, 0 means rightOf
* @type Number (integer, 0|1)
* @version 1.0 (2007-04-30)
*/
function leftOfTest(pointx,pointy,linex1,liney1,linex2,liney2) {
var result = (liney1 - pointy) * (linex2 - linex1) - (linex1 - pointx) * (liney2 - liney1);
if (result < 0) {
var leftof = 1; //case left of
}
else {
var leftof = 0; //case left of
}
return leftof;
}
/**
* calculates the distance between a given point and a given line
* @param {Number} pointx the x position of the given point
* @param {Number} pointy the y position of the given point
* @param {Number} linex1 the x position of line's start point
* @param {Number} liney1 the y position of line's start point
* @param {Number} linex2 the x position of line's end point
* @param {Number} liney2 the y position of line's end point
* @return distance the result of the leftOfTest, 1 means leftOf, 0 means rightOf
* @type Number
* @version 1.0 (2007-04-30)
*/
function distFromLine(xpoint,ypoint,linex1,liney1,linex2,liney2) {
var dx = linex2 - linex1;
var dy = liney2 - liney1;
var distance = (dy * (xpoint - linex1) - dx * (ypoint - liney1)) / Math.sqrt(Math.pow(dx,2) + Math.pow(dy,2));
return distance;
}
/**
* calculates the angle between two vectors (lines)
* @param {Number} ax the x part of vector a
* @param {Number} ay the y part of vector a
* @param {Number} bx the x part of vector b
* @param {Number} by the y part of vector b
* @return angle the angle in radians
* @type Number
* @version 1.0 (2007-04-30)
* @credits <a href="http://www.mathe-online.at/mathint/vect2/i.html#Winkel">Mathe Online (Winkel)</a>
*/
function angleBetwTwoLines(ax,ay,bx,by) {
var angle = Math.acos((ax * bx + ay * by) / (Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)) * Math.sqrt(Math.pow(bx,2) + Math.pow(by,2))));
return angle;
}
/**
* calculates the bisector vector for two given vectors
* @param {Number} ax the x part of vector a
* @param {Number} ay the y part of vector a
* @param {Number} bx the x part of vector b
* @param {Number} by the y part of vector b
* @return c the resulting vector as an Array, c[0] is the x part of the vector, c[1] is the y part
* @type Array
* @version 1.0 (2007-04-30)
* @credits <a href="http://www.mathe-online.at/mathint/vect1/i.html#Winkelsymmetrale">Mathe Online (Winkelsymmetrale)</a>
* see #calcBisectorAngle
* */
function calcBisectorVector(ax,ay,bx,by) {
var betraga = Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2));
var betragb = Math.sqrt(Math.pow(bx,2) + Math.pow(by,2));
var c = new Array();
c[0] = ax / betraga + bx / betragb;
c[1] = ay / betraga + by / betragb;
return c;
}
/**
* calculates the bisector angle for two given vectors
* @param {Number} ax the x part of vector a
* @param {Number} ay the y part of vector a
* @param {Number} bx the x part of vector b
* @param {Number} by the y part of vector b
* @return angle the bisector angle in radians
* @type Number
* @version 1.0 (2007-04-30)
* @credits <a href="http://www.mathe-online.at/mathint/vect1/i.html#Winkelsymmetrale">Mathe Online (Winkelsymmetrale)</a>
* see #calcBisectorVector
* */
function calcBisectorAngle(ax,ay,bx,by) {
var betraga = Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2));
var betragb = Math.sqrt(Math.pow(bx,2) + Math.pow(by,2));
var c1 = ax / betraga + bx / betragb;
var c2 = ay / betraga + by / betragb;
var angle = toPolarDir(c1,c2);
return angle;
}
/**
* calculates the intersection point of two given lines
* @param {Number} line1x1 the x the start point of line 1
* @param {Number} line1y1 the y the start point of line 1
* @param {Number} line1x2 the x the end point of line 1
* @param {Number} line1y2 the y the end point of line 1
* @return interSectPoint the intersection point, interSectPoint.x contains x-part, interSectPoint.y the y-part of the resulting coordinate
* @type Object
* @version 1.0 (2007-04-30)
* @credits <a href="http://astronomy.swin.edu.au/~pbourke/geometry/lineline2d/">P. Bourke</a>
*/
function intersect2lines(line1x1,line1y1,line1x2,line1y2,line2x1,line2y1,line2x2,line2y2) {
var interSectPoint = new Object();
var denominator = (line2y2 - line2y1)*(line1x2 - line1x1) - (line2x2 - line2x1)*(line1y2 - line1y1);
if (denominator == 0) {
alert("lines are parallel");
}
else {
var ua = ((line2x2 - line2x1)*(line1y1 - line2y1) - (line2y2 - line2y1)*(line1x1 - line2x1)) / denominator;
var ub = ((line1x2 - line1x1)*(line1y1 - line2y1) - (line1y2 - line1y1)*(line1x1 - line2x1)) / denominator;
}
interSectPoint["x"] = line1x1 + ua * (line1x2 - line1x1);
interSectPoint["y"] = line1y1 + ua * (line1y2 - line1y1);
return interSectPoint;
}
/**
* reformats a given number to a string by adding separators at every third digit
* @param {String|Number} inputNumber the input number, can be of type number or string
* @param {String} separator the separator, e.g. ' or ,
* @return newString the intersection point, interSectPoint.x contains x-part, interSectPoint.y the y-part of the resulting coordinate
* @type String
* @version 1.0 (2007-04-30)
*/
function formatNumberString(inputNumber,separator) {
//check if of type string, if number, convert it to string
if (typeof(inputNumber) == "Number") {
var myTempString = inputNumber.toString();
}
else {
var myTempString = inputNumber;
}
var newString="";
//if it contains a comma, it will be split
var splitResults = myTempString.split(".");
var myCounter = splitResults[0].length;
if (myCounter > 3) {
while(myCounter > 0) {
if (myCounter > 3) {
newString = separator + splitResults[0].substr(myCounter - 3,3) + newString;
}
else {
newString = splitResults[0].substr(0,myCounter) + newString;
}
myCounter -= 3;
}
}
else {
newString = splitResults[0];
}
//concatenate if it contains a comma
if (splitResults[1]) {
newString = newString + "." + splitResults[1];
}
return newString;
}
/**
* writes a status text message out to a SVG text element's first child
* @param {String} statusText the text message to be displayed
* @version 1.0 (2007-04-30)
*/
function statusChange(statusText) {
document.getElementById("statusText").firstChild.nodeValue = "Statusbar: " + statusText;
}
/**
* scales an SVG element, requires that the element has an x and y attribute (e.g. circle, ellipse, use element, etc.)
* @param {dom::Event} evt the evt object that triggered the scaling
* @param {Number} factor the scaling factor
* @version 1.0 (2007-04-30)
*/
function scaleObject(evt,factor) {
//reference to the currently selected object
var element = evt.currentTarget;
var myX = element.getAttributeNS(null,"x");
var myY = element.getAttributeNS(null,"y");
var newtransform = "scale(" + factor + ") translate(" + (myX * 1 / factor - myX) + " " + (myY * 1 / factor - myY) +")";
element.setAttributeNS(null,'transform', newtransform);
}
/**
* returns the transformation matrix (ctm) for the given node up to the root element
* the basic use case is to provide a wrapper function for the missing SVGLocatable.getTransformToElement method (missing in ASV3)
* @param {svg::SVGTransformable} node the node reference for the SVGElement the ctm is queried
* @return CTM the current transformation matrix from the given node to the root element
* @type svg::SVGMatrix
* @version 1.0 (2007-05-01)
* @credits <a href="http://www.kevlindev.com/tutorials/basics/transformations/toUserSpace/index.htm">Kevin Lindsey (toUserSpace)</a>
* @see #getTransformToElement
*/
function getTransformToRootElement(node) {
try {
//this part is for fully conformant players (like Opera, Batik, Firefox, Safari ...)
var CTM = node.getTransformToElement(document.documentElement);
}
catch (ex) {
//this part is for ASV3 or other non-conformant players
// Initialize our CTM the node's Current Transformation Matrix
var CTM = node.getCTM();
// Work our way through the ancestor nodes stopping at the SVG Document
while ( ( node = node.parentNode ) != document ) {
// Multiply the new CTM to the one with what we have accumulated so far
CTM = node.getCTM().multiply(CTM);
}
}
return CTM;
}
/**
* returns the transformation matrix (ctm) for the given dom::Node up to a different dom::Node
* the basic use case is to provide a wrapper function for the missing SVGLocatable.getTransformToElement method (missing in ASV3)
* @param {svg::SVGTransformable} node the node reference for the element the where the ctm should be calculated from
* @param {svg::SVGTransformable} targetNode the target node reference for the element the ctm should be calculated to
* @return CTM the current transformation matrix from the given node to the target element
* @type svg::SVGMatrix
* @version 1.0 (2007-05-01)
* @credits <a href="http://www.kevlindev.com/tutorials/basics/transformations/toUserSpace/index.htm">Kevin Lindsey (toUserSpace)</a>
* @see #getTransformToRootElement
*/
function getTransformToElement(node,targetNode) {
try {
//this part is for fully conformant players
var CTM = node.getTransformToElement(targetNode);
}
catch (ex) {
//this part is for ASV3 or other non-conformant players
// Initialize our CTM the node's Current Transformation Matrix
var CTM = node.getCTM();
// Work our way through the ancestor nodes stopping at the SVG Document
while ( ( node = node.parentNode ) != targetNode ) {
// Multiply the new CTM to the one with what we have accumulated so far
CTM = node.getCTM().multiply(CTM);
}
}
return CTM;
}
/**
* converts HSV to RGB values
* @param {Number} hue the hue value (between 0 and 360)
* @param {Number} sat the saturation value (between 0 and 1)
* @param {Number} val the value value (between 0 and 1)
* @return rgbArr the rgb values (associative array or object, the keys are: red,green,blue), all values are scaled between 0 and 255
* @type Object
* @version 1.0 (2007-05-01)
* @see #rgb2hsv
*/
function hsv2rgb(hue,sat,val) {
var rgbArr = new Object();
if ( sat == 0) {
rgbArr["red"] = Math.round(val * 255);
rgbArr["green"] = Math.round(val * 255);
rgbArr["blue"] = Math.round(val * 255);
}
else {
var h = hue / 60;
var i = Math.floor(h);
var f = h - i;
if (i % 2 == 0) {
f = 1 - f;
}
var m = val * (1 - sat);
var n = val * (1 - sat * f);
switch(i) {
case 0:
rgbArr["red"] = val;
rgbArr["green"] = n;
rgbArr["blue"] = m;
break;
case 1:
rgbArr["red"] = n;
rgbArr["green"] = val;
rgbArr["blue"] = m;
break;
case 2:
rgbArr["red"] = m;
rgbArr["green"] = val;
rgbArr["blue"] = n;
break;
case 3:
rgbArr["red"] = m;
rgbArr["green"] = n;
rgbArr["blue"] = val;
break;
case 4:
rgbArr["red"] = n;
rgbArr["green"] = m;
rgbArr["blue"] = val;
break;
case 5:
rgbArr["red"] = val;
rgbArr["green"] = m;
rgbArr["blue"] = n;
break;
case 6:
rgbArr["red"] = val;
rgbArr["green"] = n;
rgbArr["blue"] = m;
break;
}
rgbArr["red"] = Math.round(rgbArr["red"] * 255);
rgbArr["green"] = Math.round(rgbArr["green"] * 255);
rgbArr["blue"] = Math.round(rgbArr["blue"] * 255);
}
return rgbArr;
}
/**
* converts RGB to HSV values
* @param {Number} red the hue value (between 0 and 255)
* @param {Number} green the saturation value (between 0 and 255)
* @param {Number} blue the value value (between 0 and 255)
* @return hsvArr the hsv values (associative array or object, the keys are: hue (0-360),sat (0-1),val (0-1))
* @type Object
* @version 1.0 (2007-05-01)
* @see #hsv2rgb
*/
function rgb2hsv(red,green,blue) {
var hsvArr = new Object();
red = red / 255;
green = green / 255;
blue = blue / 255;
myMax = Math.max(red, Math.max(green,blue));
myMin = Math.min(red, Math.min(green,blue));
v = myMax;
if (myMax > 0) {
s = (myMax - myMin) / myMax;
}
else {
s = 0;
}
if (s > 0) {
myDiff = myMax - myMin;
rc = (myMax - red) / myDiff;
gc = (myMax - green) / myDiff;
bc = (myMax - blue) / myDiff;
if (red == myMax) {
h = (bc - gc) / 6;
}
if (green == myMax) {
h = (2 + rc - bc) / 6;
}
if (blue == myMax) {
h = (4 + gc - rc) / 6;
}
}
else {
h = 0;
}
if (h < 0) {
h += 1;
}
hsvArr["hue"] = Math.round(h * 360);
hsvArr["sat"] = s;
hsvArr["val"] = v;
return hsvArr;
}
/**
* populates an array such that it can be addressed by both a key or an index nr,
* note that both Arrays need to be of the same length
* @param {Array} arrayKeys the array containing the keys
* @param {Array} arrayValues the array containing the values
* @return returnArray the resulting array containing both associative values and also a regular indexed array
* @type Array
* @version 1.0 (2007-05-01)
*/
function arrayPopulate(arrayKeys,arrayValues) {
var returnArray = new Array();
if (arrayKeys.length != arrayValues.length) {
alert("error: arrays do not have the same length!");
}
else {
for (i=0;i<arrayKeys.length;i++) {
returnArray[arrayKeys[i]] = arrayValues[i];
}
}
return returnArray;
}
/**
* Wrapper object for network requests, uses getURL or XMLHttpRequest depending on availability
* The callBackFunction receives a XML or text node representing the rootElement
* of the fragment received or the return text, depending on the returnFormat.
* See also the following <a href="http://www.carto.net/papers/svg/network_requests/">documentation</a>.
* @class this is a wrapper object to provide network request functionality (get|post)
* @param {String} url the URL/IRI of the network resource to be called
* @param {Function|Object} callBackFunction the callBack function or object that is called after the data was received, in case of an object, the method 'receiveData' is called; both the function and the object's 'receiveData' method get 2 return parameters: 'node.firstChild'|text (the root element of the XML or text resource), this.additionalParams (if defined)
* @param {String} returnFormat the return format, either 'xml' or 'json' (or text)
* @param {String} method the method of the network request, either 'get' or 'post'
* @param {String|Undefined} postText the String containing the post text (optional) or Undefined (if not a 'post' request)
* @param {Object|Array|String|Number|Undefined} additionalParams additional parameters that will be passed to the callBackFunction or object (optional) or Undefined
* @return a new getData instance
* @type getData
* @constructor
* @version 1.0 (2007-02-23)
*/
function getData(url,callBackFunction,returnFormat,method,postText,additionalParams) {
this.url = url;
this.callBackFunction = callBackFunction;
this.returnFormat = returnFormat;
this.method = method;
this.additionalParams = additionalParams;
if (method != "get" && method != "post") {
alert("Error in network request: parameter 'method' must be 'get' or 'post'");
}
this.postText = postText;
this.xmlRequest = null; //@private reference to the XMLHttpRequest object
}
/**
* triggers the network request defined in the constructor
*/
getData.prototype.getData = function() {
//call getURL() if available
if (window.getURL) {
if (this.method == "get") {
getURL(this.url,this);
}
if (this.method == "post") {
postURL(this.url,this.postText,this);
}
}
//or call XMLHttpRequest() if available
else if (window.XMLHttpRequest) {
var _this = this;
this.xmlRequest = new XMLHttpRequest();
if (this.method == "get") {
if (this.returnFormat == "xml") {
this.xmlRequest.overrideMimeType("text/xml");
}
this.xmlRequest.open("GET",this.url,true);
}
if (this.method == "post") {
this.xmlRequest.open("POST",this.url,true);
}
this.xmlRequest.onreadystatechange = function() {_this.handleEvent()};
if (this.method == "get") {
this.xmlRequest.send(null);
}
if (this.method == "post") {
//test if postText exists and is of type string
var reallyPost = true;
if (!this.postText) {
reallyPost = false;
alert("Error in network post request: missing parameter 'postText'!");
}
if (typeof(this.postText) != "string") {
reallyPost = false;
alert("Error in network post request: parameter 'postText' has to be of type 'string')");
}
if (reallyPost) {
this.xmlRequest.send(this.postText);
}
}
}
//write an error message if neither method is available
else {
alert("your browser/svg viewer neither supports window.getURL nor window.XMLHttpRequest!");
}
}
/**
* this is the callback method for the getURL() or postURL() case
* @private
*/
getData.prototype.operationComplete = function(data) {
//check if data has a success property
if (data.success) {
//parse content of the XML format to the variable "node"
if (this.returnFormat == "xml") {
//convert the text information to an XML node and get the first child
var node = parseXML(data.content,document);
//distinguish between a callback function and an object
if (typeof(this.callBackFunction) == "function") {
this.callBackFunction(node.firstChild,this.additionalParams);
}
if (typeof(this.callBackFunction) == "object") {
this.callBackFunction.receiveData(node.firstChild,this.additionalParams);
}
}
if (this.returnFormat == "json") {
if (typeof(this.callBackFunction) == "function") {
this.callBackFunction(data.content,this.additionalParams);
}
if (typeof(this.callBackFunction) == "object") {
this.callBackFunction.receiveData(data.content,this.additionalParams);
}
}
}
else {
alert("something went wrong with dynamic loading of geometry!");
}
}
/**
* this is the callback method for the XMLHttpRequest case
* @private
*/
getData.prototype.handleEvent = function() {
if (this.xmlRequest.readyState == 4) {
if (this.returnFormat == "xml") {
//we need to import the XML node first
var importedNode = document.importNode(this.xmlRequest.responseXML.documentElement,true);
if (typeof(this.callBackFunction) == "function") {
this.callBackFunction(importedNode,this.additionalParams);
}
if (typeof(this.callBackFunction) == "object") {
this.callBackFunction.receiveData(importedNode,this.additionalParams);
}
}
if (this.returnFormat == "json") {
if (typeof(this.callBackFunction) == "function") {
this.callBackFunction(this.xmlRequest.responseText,this.additionalParams);
}
if (typeof(this.callBackFunction) == "object") {
this.callBackFunction.receiveData(this.xmlRequest.responseText,this.additionalParams);
}
}
}
}
/**
* Serializes an XML node and returns a string representation. Wrapper function to hide implementation differences.
* This can be used for debugging purposes or to post data to a server or network resource.
* @param {dom::Node} node the DOM node reference
* @return textRepresentation the String representation of the XML node
* @type String
* @version 1.0 (2007-05-01)
* @see getData
*/
function serializeNode(node) {
if (typeof XMLSerializer != 'undefined') {
return new XMLSerializer().serializeToString(node);
}
else if (typeof node.xml != 'undefined') {
return node.xml;
}
else if (typeof printNode != 'undefined') {
return printNode(node);
}
else if (typeof Packages != 'undefined') {
try {
var stringWriter = new java.io.StringWriter();
Packages.org.apache.batik.dom.util.DOMUtilities.writeNode(node,stringWriter);
return stringWriter.toString();
}
catch (e) {
alert("Sorry, your SVG viewer does not support the printNode/serialize function.");
return '';
}
}
else {
alert("Sorry, your SVG viewer does not support the printNode/serialize function.");
return '';
}
}
/**
* Starts a SMIL animation element with the given id by triggering the '.beginElement()' method.
* This is a convenience (shortcut) function.
* @param {String} id a valid id of a valid SMIL animation element
* @version 1.0 (2007-05-01)
*/
//starts an animtion with the given id
//this function is useful in combination with window.setTimeout()
function startAnimation(id) {
document.getElementById(id).beginElement();
}
static/scripts/timer.js
Executable
+74
View File
@@ -0,0 +1,74 @@
// source/credits: "Algorithm": http://www.codingforums.com/showthread.php?s=&threadid=10531
// The constructor should be called with
// the parent object (optional, defaults to window).
function Timer(){
this.obj = (arguments.length)?arguments[0]:window;
return this;
}
// The set functions should be called with:
// - The name of the object method (as a string) (required)
// - The millisecond delay (required)
// - Any number of extra arguments, which will all be
// passed to the method when it is evaluated.
Timer.prototype.setInterval = function(func, msec){
var i = Timer.getNew();
var t = Timer.buildCall(this.obj, i, arguments);
Timer.set[i].timer = window.setInterval(t,msec);
return i;
}
Timer.prototype.setTimeout = function(func, msec){
var i = Timer.getNew();
Timer.buildCall(this.obj, i, arguments);
Timer.set[i].timer = window.setTimeout("Timer.callOnce("+i+");",msec);
return i;
}
// The clear functions should be called with
// the return value from the equivalent set function.
Timer.prototype.clearInterval = function(i){
if(!Timer.set[i]) return;
window.clearInterval(Timer.set[i].timer);
Timer.set[i] = null;
}
Timer.prototype.clearTimeout = function(i){
if(!Timer.set[i]) return;
window.clearTimeout(Timer.set[i].timer);
Timer.set[i] = null;
}
// Private data
Timer.set = new Array();
Timer.buildCall = function(obj, i, args){
var t = "";
Timer.set[i] = new Array();
if(obj != window){
Timer.set[i].obj = obj;
t = "Timer.set["+i+"].obj.";
}
t += args[0]+"(";
if(args.length > 2){
Timer.set[i][0] = args[2];
t += "Timer.set["+i+"][0]";
for(var j=1; (j+2)<args.length; j++){
Timer.set[i][j] = args[j+2];
t += ", Timer.set["+i+"]["+j+"]";
}}
t += ");";
Timer.set[i].call = t;
return t;
}
Timer.callOnce = function(i){
if(!Timer.set[i]) return;
eval(Timer.set[i].call);
Timer.set[i] = null;
}
Timer.getNew = function(){
var i = 0;
while(Timer.set[i]) i++;
return i;
}
tools/rgenetics/rgGRR.py
+1145 -1096
View File
File diff suppressed because it is too large Load Diff
tools/rgenetics/rgManQQ.py
+13 -6
View File
@@ -129,12 +129,12 @@ dn = names(rawd)
cc = dn[chromcolumn]
oc = dn[offsetcolumn]
nams = c(cc,oc)
d = rawd[do.call(order,rawd[nams]),]
# mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according.html
# in case not yet ordered
print(paste('###',length(d[,1]),'values read from',infile,'read - now running plots',sep=' '))
for (pvalscolumn in pvalscolumns) {
if (pvalscolumn > 0)
plen = length(d[,1])
doreorder=True
print(paste('###',plen,'values read from',infile,'read - now running plots',sep=' '))
if (plen > 0) {
for (pvalscolumn in pvalscolumns) {
if (pvalscolumn > 0)
{
cname = names(d)[pvalscolumn]
mytitle = paste('p=',cname,', ',title,sep='')
@@ -142,6 +142,12 @@ if (pvalscolumn > 0)
myqqplot = qq(d[,pvalscolumn],title=mytitle)
print(paste('## qqplot on',cname,'done'))
if ((chromcolumn > 0) & (offsetcolumn > 0)) {
if (doreorder) {
d = rawd[do.call(order,rawd[nams]),]
# mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according.html
# in case not yet ordered
doreorder = False
}
print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn))
mymanplot= manhattan(chrom=d[,chromcolumn],offset=d[,offsetcolumn],pvals=d[,pvalscolumn],title=mytitle,grey=grey)
print(paste('## manhattan plot on',cname,'done'))
@@ -157,6 +163,7 @@ if (pvalscolumn > 0)
print(paste('pvalue column =',pvalscolumn,'Cannot parse it so no plots possible'))
}
} # for pvalscolumn
} else { print('## Problem - no values available to plot - was there really a chromosome and offset column?') }
}
rgqqMan()