[galaxy-dev] [hg] galaxy 3633: Add the raw uncompressed .js files needed for ...
Greg Von Kuster
greg at bx.psu.edu
Thu Apr 15 20:19:19 EDT 2010
details: http://www.bx.psu.edu/hg/galaxy/rev/0b682d3dd01b
changeset: 3633:0b682d3dd01b
user: fubar: ross Lazarus at gmail period com
date: Tue Apr 13 11:15:35 2010 -0400
description:
Add the raw uncompressed .js files needed for rgGRR svg display - the packed ones were already there
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.
diffstat:
static/scripts/checkbox_and_radiobutton.js | 347 ++++
static/scripts/helper_functions.js | 817 ++++++++++
static/scripts/timer.js | 74 +
tools/rgenetics/rgGRR.py | 2241 ++++++++++++++-------------
tools/rgenetics/rgManQQ.py | 19 +-
5 files changed, 2396 insertions(+), 1102 deletions(-)
diffs (truncated from 3540 to 3000 lines):
diff -r 0dc1fc63c945 -r 0b682d3dd01b static/scripts/checkbox_and_radiobutton.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/static/scripts/checkbox_and_radiobutton.js Tue Apr 13 11:15:35 2010 -0400
@@ -0,0 +1,347 @@
+/*
+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 at 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 at 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;
+ }
+}
\ No newline at end of file
diff -r 0dc1fc63c945 -r 0b682d3dd01b static/scripts/helper_functions.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/static/scripts/helper_functions.js Tue Apr 13 11:15:35 2010 -0400
@@ -0,0 +1,817 @@
+/**
+ * @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 at 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 at 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 at 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();
+}
diff -r 0dc1fc63c945 -r 0b682d3dd01b static/scripts/timer.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/static/scripts/timer.js Tue Apr 13 11:15:35 2010 -0400
@@ -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;
+}
\ No newline at end of file
diff -r 0dc1fc63c945 -r 0b682d3dd01b tools/rgenetics/rgGRR.py
--- a/tools/rgenetics/rgGRR.py Tue Apr 13 10:22:27 2010 -0400
+++ b/tools/rgenetics/rgGRR.py Tue Apr 13 11:15:35 2010 -0400
@@ -1,1096 +1,1145 @@
-"""
-# july 2009: Need to see outliers so need to draw them last?
-# could use clustering on the zscores to guess real relationships for unrelateds
-# but definitely need to draw last
-# added MAX_SHOW_ROWS to limit the length of the main report page
-# Changes for Galaxy integration
-# added more robust knuth method for one pass mean and sd
-# no difference really - let's use scipy.mean() and scipy.std() instead...
-# fixed labels and changed to .xls for outlier reports so can open in excel
-# interesting - with a few hundred subjects, 5k gives good resolution
-# and 100k gives better but not by much
-# TODO remove non autosomal markers
-# TODO it would be best if label had the zmean and zsd as these are what matter for
-# outliers rather than the group mean/sd
-# mods to rgGRR.py from channing CVS which John Ziniti has rewritten to produce SVG plots
-# to make a Galaxy tool - we need the table of mean and SD for interesting pairs, the SVG and the log
-# so the result should be an HTML file
-
-# rgIBS.py
-# use a random subset of markers for a quick ibs
-# to identify sample dups and closely related subjects
-# try snpMatrix and plink and see which one works best for us?
-# abecasis grr plots mean*sd for every subject to show clusters
-# mods june 23 rml to avoid non-autosomal markers
-# we seem to be distinguishing parent-child by gender - 2 clouds!
-
-
-snpMatrix from David Clayton has:
-ibs.stats function to calculate the identity-by-state stats of a group of samples
-Description
-Given a snp.matrix-class or a X.snp.matrix-class object with N samples, calculates some statistics
-about the relatedness of every pair of samples within.
-
-Usage
-ibs.stats(x)
-8 ibs.stats
-Arguments
-x a snp.matrix-class or a X.snp.matrix-class object containing N samples
-Details
-No-calls are excluded from consideration here.
-Value
-A data.frame containing N(N - 1)/2 rows, where the row names are the sample name pairs separated
-by a comma, and the columns are:
-Count count of identical calls, exclusing no-calls
-Fraction fraction of identical calls comparied to actual calls being made in both samples
-Warning
-In some applications, it may be preferable to subset a (random) selection of SNPs first - the
-calculation
-time increases as N(N - 1)M/2 . Typically for N = 800 samples and M = 3000 SNPs, the
-calculation time is about 1 minute. A full GWA scan could take hours, and quite unnecessary for
-simple applications such as checking for duplicate or related samples.
-Note
-This is mostly written to find mislabelled and/or duplicate samples.
-Illumina indexes their SNPs in alphabetical order so the mitochondria SNPs comes first - for most
-purpose it is undesirable to use these SNPs for IBS purposes.
-TODO: Worst-case S4 subsetting seems to make 2 copies of a large object, so one might want to
-subset before rbind(), etc; a future version of this routine may contain a built-in subsetting facility
-"""
-import sys,os,time,random,string,copy,optparse
-
-try:
- set
-except NameError:
- from Sets import Set as set
-
-from rgutils import timenow
-import plinkbinJZ
-
-
-opts = None
-verbose = False
-
-showPolygons = False
-
-class NullDevice:
- def write(self, s):
- pass
-
-tempstderr = sys.stderr # save
-sys.stderr = NullDevice()
-# need to avoid blather about deprecation and other strange stuff from scipy
-# the current galaxy job runner assumes that
-# the job is in error if anything appears on sys.stderr
-# grrrrr. James wants to keep it that way instead of using the
-# status flag for some strange reason. Presumably he doesn't use R or (in this case, scipy)
-import numpy
-import scipy
-from scipy import weave
-
-
-sys.stderr=tempstderr
-
-
-PROGNAME = os.path.split(sys.argv[0])[-1]
-X_AXIS_LABEL = 'Mean Alleles Shared'
-Y_AXIS_LABEL = 'SD Alleles Shared'
-LEGEND_ALIGN = 'topleft'
-LEGEND_TITLE = 'Relationship'
-DEFAULT_SYMBOL_SIZE = 1.0 # default symbol size
-DEFAULT_SYMBOL_SIZE = 0.5 # default symbol size
-
-### Some colors for R/rpy
-R_BLACK = 1
-R_RED = 2
-R_GREEN = 3
-R_BLUE = 4
-R_CYAN = 5
-R_PURPLE = 6
-R_YELLOW = 7
-R_GRAY = 8
-
-### ... and some point-styles
-
-###
-PLOT_HEIGHT = 600
-PLOT_WIDTH = 1150
-
-
-#SVG_COLORS = ('black', 'darkblue', 'blue', 'deepskyblue', 'firebrick','maroon','crimson')
-#SVG_COLORS = ('cyan','dodgerblue','mediumpurple', 'fuchsia', 'red','gold','gray')
-SVG_COLORS = ('cyan','dodgerblue','mediumpurple','forestgreen', 'lightgreen','gold','gray')
-# dupe,parentchild,sibpair,halfsib,parents,unrel,unkn
-#('orange', 'red', 'green', 'chartreuse', 'blue', 'purple', 'gray')
-
-OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Rel_Mean)\tSdev(Rel_Mean)\tMean(Rel_Sdev)\tSdev(Rel_Sdev)\n'
-OUTLIERS_HEADER_list = ['Mean','Sdev','ZMean','ZSdev','FID1','IID1','FID2','IID2',
-'RGMean_M','RGMean_SD','RGSD_M','RGSD_SD']
-TABLE_HEADER='fid1 iid1\tfid2 iid2\tmean\tsdev\tzmean\tzsdev\tgeno\trelcode\n'
-
-
-### Relationship codes, text, and lookups/mappings
-N_RELATIONSHIP_TYPES = 7
-REL_DUPE, REL_PARENTCHILD, REL_SIBS, REL_HALFSIBS, REL_RELATED, REL_UNRELATED, REL_UNKNOWN = range(N_RELATIONSHIP_TYPES)
-REL_LOOKUP = {
- REL_DUPE: ('dupe', R_BLUE, 1),
- REL_PARENTCHILD: ('parentchild', R_YELLOW, 1),
- REL_SIBS: ('sibpairs', R_RED, 1),
- REL_HALFSIBS: ('halfsibs', R_GREEN, 1),
- REL_RELATED: ('parents', R_PURPLE, 1),
- REL_UNRELATED: ('unrelated', R_CYAN, 1),
- REL_UNKNOWN: ('unknown', R_GRAY, 1),
- }
-OUTLIER_STDEVS = {
- REL_DUPE: 2,
- REL_PARENTCHILD: 2,
- REL_SIBS: 2,
- REL_HALFSIBS: 2,
- REL_RELATED: 2,
- REL_UNRELATED: 3,
- REL_UNKNOWN: 2,
- }
-# note now Z can be passed in
-
-REL_STATES = [REL_LOOKUP[r][0] for r in range(N_RELATIONSHIP_TYPES)]
-REL_COLORS = SVG_COLORS
-REL_POINTS = [REL_LOOKUP[r][2] for r in range(N_RELATIONSHIP_TYPES)]
-
-DEFAULT_MAX_SAMPLE_SIZE = 10000
-
-REF_COUNT_HOM1 = 3
-REF_COUNT_HET = 2
-REF_COUNT_HOM2 = 1
-MISSING = 0
-MAX_SHOW_ROWS = 100 # framingham has millions - delays showing output page - so truncate and explain
-MARKER_PAIRS_PER_SECOND_SLOW = 15000000.0
-MARKER_PAIRS_PER_SECOND_FAST = 70000000.0
-
-
-galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
-<title></title>
-<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
-</head>
-<body>
-<div class="document">
-"""
-
-
-SVG_HEADER = '''<?xml version="1.0" standalone="no"?>
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.2//EN" "http://www.w3.org/Graphics/SVG/1.2/DTD/svg12.dtd">
-
-<svg width="1280" height="800"
- xmlns="http://www.w3.org/2000/svg" version="1.2"
- xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()">
-
- <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/checkbox_and_radiobutton.js"/>
- <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/helper_functions.js"/>
- <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/timer.js"/>
- <script type="text/ecmascript">
- <![CDATA[
- var checkBoxes = new Array();
- var radioGroupBandwidth;
- var colours = ['%s','%s','%s','%s','%s','%s','%s'];
- function init() {
- var style = {"font-family":"Arial,Helvetica", "fill":"black", "font-size":12};
- var dist = 12;
- var yOffset = 4;
-
- //A checkBox for each relationship type dupe,parentchild,sibpair,halfsib,parents,unrel,unkn
- checkBoxes["dupe"] = new checkBox("dupe","checkboxes",20,40,"cbRect","cbCross",true,"Duplicate",style,dist,yOffset,undefined,hideShowLayer);
- checkBoxes["parentchild"] = new checkBox("parentchild","checkboxes",20,60,"cbRect","cbCross",true,"Parent-Child",style,dist,yOffset,undefined,hideShowLayer);
- checkBoxes["sibpairs"] = new checkBox("sibpairs","checkboxes",20,80,"cbRect","cbCross",true,"Sib-pairs",style,dist,yOffset,undefined,hideShowLayer);
- checkBoxes["halfsibs"] = new checkBox("halfsibs","checkboxes",20,100,"cbRect","cbCross",true,"Half-sibs",style,dist,yOffset,undefined,hideShowLayer);
- checkBoxes["parents"] = new checkBox("parents","checkboxes",20,120,"cbRect","cbCross",true,"Parents",style,dist,yOffset,undefined,hideShowLayer);
- checkBoxes["unrelated"] = new checkBox("unrelated","checkboxes",20,140,"cbRect","cbCross",true,"Unrelated",style,dist,yOffset,undefined,hideShowLayer);
- checkBoxes["unknown"] = new checkBox("unknown","checkboxes",20,160,"cbRect","cbCross",true,"Unknown",style,dist,yOffset,undefined,hideShowLayer);
-
- }
-
- function hideShowLayer(id, status, label) {
- var vis = "hidden";
- if (status) {
- vis = "visible";
- }
- document.getElementById(id).setAttributeNS(null, 'visibility', vis);
- }
-
- function showBTT(evt, rel, mm, dm, md, dd, n, mg, dg, lg, hg) {
- var x = parseInt(evt.pageX)-250;
- var y = parseInt(evt.pageY)-110;
- switch(rel) {
- case 0:
- fill = colours[rel];
- relt = "dupe";
- break;
- case 1:
- fill = colours[rel];
- relt = "parentchild";
- break;
- case 2:
- fill = colours[rel];
- relt = "sibpairs";
- break;
- case 3:
- fill = colours[rel];
- relt = "halfsibs";
- break;
- case 4:
- fill = colours[rel];
- relt = "parents";
- break;
- case 5:
- fill = colours[rel];
- relt = "unrelated";
- break;
- case 6:
- fill = colours[rel];
- relt = "unknown";
- break;
- default:
- fill = "cyan";
- relt = "ERROR_CODE: "+rel;
- }
-
- document.getElementById("btRel").textContent = "GROUP: "+relt;
- document.getElementById("btMean").textContent = "mean="+mm+" +/- "+dm;
- document.getElementById("btSdev").textContent = "sdev="+dm+" +/- "+dd;
- document.getElementById("btPair").textContent = "npairs="+n;
- document.getElementById("btGeno").textContent = "ngenos="+mg+" +/- "+dg+" (min="+lg+", max="+hg+")";
- document.getElementById("btHead").setAttribute('fill', fill);
-
- var tt = document.getElementById("btTip");
- tt.setAttribute("transform", "translate("+x+","+y+")");
- tt.setAttribute('visibility', 'visible');
- }
-
- function showOTT(evt, rel, s1, s2, mean, sdev, ngeno, rmean, rsdev) {
- var x = parseInt(evt.pageX)-150;
- var y = parseInt(evt.pageY)-180;
-
- switch(rel) {
- case 0:
- fill = colours[rel];
- relt = "dupe";
- break;
- case 1:
- fill = colours[rel];
- relt = "parentchild";
- break;
- case 2:
- fill = colours[rel];
- relt = "sibpairs";
- break;
- case 3:
- fill = colours[rel];
- relt = "halfsibs";
- break;
- case 4:
- fill = colours[rel];
- relt = "parents";
- break;
- case 5:
- fill = colours[rel];
- relt = "unrelated";
- break;
- case 6:
- fill = colours[rel];
- relt = "unknown";
- break;
- default:
- fill = "cyan";
- relt = "ERROR_CODE: "+rel;
- }
-
- document.getElementById("otRel").textContent = "PAIR: "+relt;
- document.getElementById("otS1").textContent = "s1="+s1;
- document.getElementById("otS2").textContent = "s2="+s2;
- document.getElementById("otMean").textContent = "mean="+mean;
- document.getElementById("otSdev").textContent = "sdev="+sdev;
- document.getElementById("otGeno").textContent = "ngenos="+ngeno;
- document.getElementById("otRmean").textContent = "relmean="+rmean;
- document.getElementById("otRsdev").textContent = "relsdev="+rsdev;
- document.getElementById("otHead").setAttribute('fill', fill);
-
- var tt = document.getElementById("otTip");
- tt.setAttribute("transform", "translate("+x+","+y+")");
- tt.setAttribute('visibility', 'visible');
- }
-
- function hideBTT(evt) {
- document.getElementById("btTip").setAttributeNS(null, 'visibility', 'hidden');
- }
-
- function hideOTT(evt) {
- document.getElementById("otTip").setAttributeNS(null, 'visibility', 'hidden');
- }
-
- ]]>
- </script>
- <defs>
- <!-- symbols for check boxes -->
- <symbol id="cbRect" overflow="visible">
- <rect x="-5" y="-5" width="10" height="10" fill="white" stroke="dimgray" stroke-width="1" cursor="pointer"/>
- </symbol>
- <symbol id="cbCross" overflow="visible">
- <g pointer-events="none" stroke="black" stroke-width="1">
- <line x1="-3" y1="-3" x2="3" y2="3"/>
- <line x1="3" y1="-3" x2="-3" y2="3"/>
- </g>
- </symbol>
- </defs>
-
-<desc>Developer Works Dynamic Scatter Graph Scaling Example</desc>
-
-<!-- Now Draw the main X and Y axis -->
-<g style="stroke-width:1.0; stroke:black; shape-rendering:crispEdges">
- <!-- X Axis top and bottom -->
- <path d="M 100 100 L 1250 100 Z"/>
- <path d="M 100 700 L 1250 700 Z"/>
-
- <!-- Y Axis left and right -->
- <path d="M 100 100 L 100 700 Z"/>
- <path d="M 1250 100 L 1250 700 Z"/>
-</g>
-
-<g transform="translate(100,100)">
-
- <!-- Grid Lines -->
- <g style="fill:none; stroke:#dddddd; stroke-width:1; stroke-dasharray:2,2; text-anchor:end; shape-rendering:crispEdges">
-
- <!-- Vertical grid lines -->
- <line x1="125" y1="0" x2="115" y2="600" />
- <line x1="230" y1="0" x2="230" y2="600" />
- <line x1="345" y1="0" x2="345" y2="600" />
- <line x1="460" y1="0" x2="460" y2="600" />
- <line x1="575" y1="0" x2="575" y2="600" style="stroke-dasharray:none;" />
- <line x1="690" y1="0" x2="690" y2="600" />
- <line x1="805" y1="0" x2="805" y2="600" />
- <line x1="920" y1="0" x2="920" y2="600" />
- <line x1="1035" y1="0" x2="1035" y2="600" />
-
- <!-- Horizontal grid lines -->
- <line x1="0" y1="60" x2="1150" y2="60" />
- <line x1="0" y1="120" x2="1150" y2="120" />
- <line x1="0" y1="180" x2="1150" y2="180" />
- <line x1="0" y1="240" x2="1150" y2="240" />
- <line x1="0" y1="300" x2="1150" y2="300" style="stroke-dasharray:none;" />
- <line x1="0" y1="360" x2="1150" y2="360" />
- <line x1="0" y1="420" x2="1150" y2="420" />
- <line x1="0" y1="480" x2="1150" y2="480" />
- <line x1="0" y1="540" x2="1150" y2="540" />
- </g>
-
- <!-- Legend -->
- <g style="fill:black; stroke:none" font-size="12" font-family="Arial" transform="translate(25,25)">
- <rect width="160" height="270" style="fill:none; stroke:black; shape-rendering:crispEdges" />
- <text x="5" y="20" style="fill:black; stroke:none;" font-size="13" font-weight="bold">Given Pair Relationship</text>
- <rect x="120" y="35" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
- <rect x="120" y="55" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
- <rect x="120" y="75" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
- <rect x="120" y="95" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
- <rect x="120" y="115" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
- <rect x="120" y="135" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
- <rect x="120" y="155" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
- <text x="15" y="195" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore gt 15</text>
- <circle cx="125" cy="192" r="6" style="stroke:red; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
- <text x="15" y="215" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore 4 to 15</text>
- <circle cx="125" cy="212" r="3" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
- <text x="15" y="235" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore lt 4</text>
- <circle cx="125" cy="232" r="2" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
- <g id="checkboxes">
- </g>
- </g>
-
-
- <g style='fill:black; stroke:none' font-size="17" font-family="Arial">
- <!-- X Axis Labels -->
- <text x="480" y="660">Mean Alleles Shared</text>
- <text x="0" y="630" >1.0</text>
- <text x="277" y="630" >1.25</text>
- <text x="564" y="630" >1.5</text>
- <text x="842" y="630" >1.75</text>
- <text x="1140" y="630" >2.0</text>
- </g>
-
- <g transform="rotate(270)" style="fill:black; stroke:none" font-size="17" font-family="Arial">
- <!-- Y Axis Labels -->
- <text x="-350" y="-40">SD Alleles Shared</text>
- <text x="-20" y="-10" >1.0</text>
- <text x="-165" y="-10" >0.75</text>
- <text x="-310" y="-10" >0.5</text>
- <text x="-455" y="-10" >0.25</text>
- <text x="-600" y="-10" >0.0</text>
- </g>
-
-<!-- Plot Title -->
-<g style="fill:black; stroke:none" font-size="18" font-family="Arial">
- <text x="425" y="-30">%s</text>
-</g>
-
-<!-- One group/layer of points for each relationship type -->
-'''
-
-SVG_FOOTER = '''
-<!-- End of Data -->
-</g>
-<g id="btTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial">
- <rect width="250" height="110" style="fill:silver" rx="2" ry="2"/>
- <rect id="btHead" width="250" height="20" rx="2" ry="2" />
- <text id="btRel" y="14" x="85">unrelated</text>
- <text id="btMean" y="40" x="4">mean=1.5 +/- 0.04</text>
- <text id="btSdev" y="60" x="4">sdev=0.7 +/- 0.03</text>
- <text id="btPair" y="80" x="4">npairs=1152</text>
- <text id="btGeno" y="100" x="4">ngenos=4783 +/- 24 (min=1000, max=5000)</text>
-</g>
-
-<g id="otTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial">
- <rect width="150" height="180" style="fill:silver" rx="2" ry="2"/>
- <rect id="otHead" width="150" height="20" rx="2" ry="2" />
- <text id="otRel" y="14" x="40">sibpairs</text>
- <text id="otS1" y="40" x="4">s1=fid1,iid1</text>
- <text id="otS2" y="60" x="4">s2=fid2,iid2</text>
- <text id="otMean" y="80" x="4">mean=1.82</text>
- <text id="otSdev" y="100" x="4">sdev=0.7</text>
- <text id="otGeno" y="120" x="4">ngeno=4487</text>
- <text id="otRmean" y="140" x="4">relmean=1.85</text>
- <text id="otRsdev" y="160" x="4">relsdev=0.65</text>
-</g>
-</svg>
-'''
-
-OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Mean)\tSdev(Mean)\tMean(Sdev)\tSdev(Sdev)\n'
-
-DEFAULT_MAX_SAMPLE_SIZE = 5000
-
-REF_COUNT_HOM1 = 3
-REF_COUNT_HET = 2
-REF_COUNT_HOM2 = 1
-MISSING = 0
-
-MARKER_PAIRS_PER_SECOND_SLOW = 15000000
-MARKER_PAIRS_PER_SECOND_FAST = 70000000
-
-POLYGONS = {
- REL_UNRELATED: ((1.360, 0.655), (1.385, 0.730), (1.620, 0.575), (1.610, 0.505)),
- REL_HALFSIBS: ((1.630, 0.500), (1.630, 0.550), (1.648, 0.540), (1.648, 0.490)),
- REL_SIBS: ((1.660, 0.510), (1.665, 0.560), (1.820, 0.410), (1.820, 0.390)),
- REL_PARENTCHILD: ((1.650, 0.470), (1.650, 0.490), (1.750, 0.440), (1.750, 0.420)),
- REL_DUPE: ((1.970, 0.000), (1.970, 0.150), (2.000, 0.150), (2.000, 0.000)),
- }
-
-def distance(point1, point2):
- """ Calculate the distance between two points
- """
- (x1,y1) = [float(d) for d in point1]
- (x2,y2) = [float(d) for d in point2]
- dx = abs(x1 - x2)
- dy = abs(y1 - y2)
- return math.sqrt(dx**2 + dy**2)
-
-def point_inside_polygon(x, y, poly):
- """ Determine if a point (x,y) is inside a given polygon or not
- poly is a list of (x,y) pairs.
-
- Taken from: http://www.ariel.com.au/a/python-point-int-poly.html
- """
-
- n = len(poly)
- inside = False
-
- p1x,p1y = poly[0]
- for i in range(n+1):
- p2x,p2y = poly[i % n]
- if y > min(p1y,p2y):
- if y <= max(p1y,p2y):
- if x <= max(p1x,p2x):
- if p1y != p2y:
- xinters = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x
- if p1x == p2x or x <= xinters:
- inside = not inside
- p1x,p1y = p2x,p2y
- return inside
-
-def readMap(pedfile):
- """
- """
- mapfile = pedfile.replace('.ped', '.map')
- marker_list = []
- if os.path.exists(mapfile):
- print 'readMap: %s' % (mapfile)
- fh = file(mapfile, 'r')
- for line in fh:
- marker_list.append(line.strip().split())
- fh.close()
- print 'readMap: %s markers' % (len(marker_list))
- return marker_list
-
-def calcMeanSD(useme):
- """
- A numerically stable algorithm is given below. It also computes the mean.
- This algorithm is due to Knuth,[1] who cites Welford.[2]
- n = 0
- mean = 0
- M2 = 0
-
- foreach x in data:
- n = n + 1
- delta = x - mean
- mean = mean + delta/n
- M2 = M2 + delta*(x - mean) // This expression uses the new value of mean
- end for
-
- variance_n = M2/n
- variance = M2/(n - 1)
- """
- mean = 0.0
- M2 = 0.0
- sd = 0.0
- n = len(useme)
- if n > 1:
- for i,x in enumerate(useme):
- delta = x - mean
- mean = mean + delta/(i+1) # knuth uses n+=1 at start
- M2 = M2 + delta*(x - mean) # This expression uses the new value of mean
- variance = M2/(n-1) # assume is sample so lose 1 DOF
- sd = pow(variance,0.5)
- return mean,sd
-
-
-def doIBSpy(inpath='',basename='',outdir=None,logf=None,
- nrsSamples=10000,title='title',pdftoo=0,Zcutoff=2.0):
- #def doIBS(pedName, title, nrsSamples=None, pdftoo=False):
- """ started with snpmatrix but GRR uses actual IBS counts and sd's
- """
- repOut = [] # text strings to add to the html display
- refallele = {}
- tblf = '%s_table.xls' % (title)
- tbl = file(os.path.join(outdir,tblf), 'w')
- tbl.write(TABLE_HEADER)
- svgf = '%s.svg' % (title)
- svg = file(os.path.join(outdir,svgf), 'w')
-
- bedname = '%s.bed' % (inpath)
- pedname = '%s.ped' % (inpath)
- print 'pedname',pedname
- if os.path.exists(bedname):
- ped = plinkbinJZ.BPed(inpath)
- ped.parse(quick=True)
- elif os.path.exists(pedname):
- ped = plinkbinJZ.LPed(inpath)
- ped.parse()
- else:
- print >> sys.stdout, '## doIBSpy problem - cannot open %s or %s - cannot run' % (bedname,pedname)
- nMarkers = len(ped._markers)
- if nMarkers < 5:
- print sys.stderr, '### ERROR - %d is too few markers for reliable estimation in %s - terminating' % (nMarkers,PROGNAME)
- sys.exit(1)
- nSubjects = len(ped._subjects)
- nrsSamples = min(nMarkers, nrsSamples)
- if opts and opts.use_mito:
- markers = range(nMarkers)
- nrsSamples = min(len(markers), nrsSamples)
- sampleIndexes = sorted(random.sample(markers, nrsSamples))
- else:
- autosomals = ped.autosomal_indices()
- nrsSamples = min(len(autosomals), nrsSamples)
- sampleIndexes = sorted(random.sample(autosomals, nrsSamples))
-
- print ''
- print 'Getting random.sample of %s from %s total' % (nrsSamples, nMarkers)
- npairs = (nSubjects*(nSubjects-1))/2 # total rows in table
- newfiles=[svgf,tblf]
- explanations = ['rgGRR Plot (requires SVG)','Mean by SD alleles shared - %d rows' % npairs]
- # these go with the output file links in the html file
- s = 'Reading genotypes for %s subjects and %s markers\n' % (nSubjects, nrsSamples)
- logf.write(s)
- minUsegenos = nrsSamples/2 # must have half?
- nGenotypes = nSubjects*nrsSamples
- stime = time.time()
- emptyRows = set()
- genos = numpy.zeros((nSubjects, nrsSamples), dtype=int)
- for s in xrange(nSubjects):
- nValid = 0
- #getGenotypesByIndices(self, s, mlist, format)
- genos[s] = ped.getGenotypesByIndices(s, sampleIndexes, format='ref')
- nValid = sum([1 for g in genos[s] if g])
- if not nValid:
- emptyRows.add(s)
- sub = ped.getSubject(s)
- print 'All missing for row %d (%s)' % (s, sub)
- logf.write('All missing for row %d (%s)\n' % (s, sub))
- rtime = time.time() - stime
- if verbose:
- print '@@Read %s genotypes in %s seconds' % (nGenotypes, rtime)
-
-
- ### Now the expensive part. For each pair of subjects, we get the mean number
- ### and standard deviation of shared alleles over all of the markers where both
- ### subjects have a known genotype. Identical subjects should have mean shared
- ### alleles very close to 2.0 with a standard deviation very close to 0.0.
- tot = nSubjects*(nSubjects-1)/2
- nprog = tot/10
- nMarkerpairs = tot * nrsSamples
- estimatedTimeSlow = nMarkerpairs/MARKER_PAIRS_PER_SECOND_SLOW
- estimatedTimeFast = nMarkerpairs/MARKER_PAIRS_PER_SECOND_FAST
-
- pairs = []
- pair_data = {}
- means = [] ## Mean IBS for each pair
- ngenoL = [] ## Count of comparable genotypes for each pair
- sdevs = [] ## Standard dev for each pair
- rels = [] ## A relationship code for each pair
- zmeans = [0.0 for x in xrange(tot)] ## zmean score for each pair for the relgroup
- zstds = [0.0 for x in xrange(tot)] ## zstd score for each pair for the relgrp
- skip = set()
- ndone = 0 ## How many have been done so far
-
- logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog))
- logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow))
-
- t1sum = 0
- t2sum = 0
- t3sum = 0
- now = time.time()
- scache = {}
- _founder_cache = {}
- C_CODE = """
- #include "math.h"
- int i;
- int sumibs = 0;
- int ssqibs = 0;
- int ngeno = 0;
- float mean = 0;
- float M2 = 0;
- float delta = 0;
- float sdev=0;
- float variance=0;
- for (i=0; i<nrsSamples; i++) {
- int a1 = g1[i];
- int a2 = g2[i];
- if (a1 != 0 && a2 != 0) {
- ngeno += 1;
- int shared = 2-abs(a1-a2);
- delta = shared - mean;
- mean = mean + delta/ngeno;
- M2 += delta*(shared-mean);
- // yes that second time, the updated mean is used see calcmeansd above;
- //printf("%d %d %d %d %d %d\\n", i, a1, a2, ngeno, shared, squared);
- }
- }
- if (ngeno > 1) {
- variance = M2/(ngeno-1);
- sdev = sqrt(variance);
- //printf("OK: %d %3.2f %3.2f\\n", ngeno, mean, sdev);
- }
- //printf("%d %d %d %1.2f %1.2f\\n", ngeno, sumibs, ssqibs, mean, sdev);
- result[0] = ngeno;
- result[1] = mean;
- result[2] = sdev;
- return_val = ngeno;
- """
- started = time.time()
- for s1 in xrange(nSubjects):
- if s1 in emptyRows:
- continue
- (fid1,iid1,did1,mid1,sex1,phe1,iid1,d_sid1,m_sid1) = scache.setdefault(s1, ped.getSubject(s1))
-
- isFounder1 = _founder_cache.setdefault(s1, (did1==mid1))
- g1 = genos[s1]
-
- for s2 in xrange(s1+1, nSubjects):
- if s2 in emptyRows:
- continue
- if nprog and ndone % nprog == 0 and ndone > 1:
- dur = time.time() - started
- pct = float(ndone)/tot*100.0
- logf.write('%f sec at pair %d of %d (%3.2f%%): %f marker*pairs/sec\n' % (dur, ndone, tot, pct, ndone/dur*nrsSamples))
- t1s = time.time()
-
- (fid2,iid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache.setdefault(s2, ped.getSubject(s2))
-
- g2 = genos[s2]
- isFounder2 = _founder_cache.setdefault(s2, (did2==mid2))
-
- # Determine the relationship for this pair
- relcode = REL_UNKNOWN
- if (fid2 == fid1):
- if iid1 == iid2:
- relcode = REL_DUPE
- elif (did2 == did1) and (mid2 == mid1) and did1 != mid1:
- relcode = REL_SIBS
- elif (iid1 == mid2) or (iid1 == did2) or (iid2 == mid1) or (iid2 == did1):
- relcode = REL_PARENTCHILD
- elif (str(did1) != '0' and (did2 == did1)) or (str(mid1) != '0' and (mid2 == mid1)):
- relcode = REL_HALFSIBS
- else:
- # People in the same family should be marked as some other
- # form of related. In general, these people will have a
- # pretty random spread of similarity. This distinction is
- # probably not very useful most of the time
- relcode = REL_RELATED
- else:
- ### Different families
- relcode = REL_UNRELATED
-
- t1e = time.time()
- t1sum += t1e-t1s
-
-
- ### Calculate sum(2-abs(a1-a2)) and sum((2-abs(a1-a2))**2) and count
- ### the number of contributing genotypes. These values are not actually
- ### calculated here, but instead are looked up in a table for speed.
- ### FIXME: This is still too slow ...
- result = [0.0, 0.0, 0.0]
- ngeno = weave.inline(C_CODE, ['g1', 'g2', 'nrsSamples', 'result'])
- if ngeno >= minUsegenos:
- _, mean, sdev = result
- means.append(mean)
- sdevs.append(sdev)
- ngenoL.append(ngeno)
- pairs.append((s1, s2))
- rels.append(relcode)
- else:
- skip.add(ndone) # signal no comparable genotypes for this pair
- ndone += 1
- t2e = time.time()
- t2sum += t2e-t1e
- t3e = time.time()
- t3sum += t3e-t2e
-
- logme = [ 'T1: %s' % (t1sum), 'T2: %s' % (t2sum), 'T3: %s' % (t3sum),'TOT: %s' % (t3e-now),
- '%s pairs with no (or not enough) comparable genotypes (%3.1f%%)' % (len(skip),
- float(len(skip))/float(tot)*100)]
- logf.write('%s\n' % '\t'.join(logme))
- ### Calculate mean and standard deviation of scores on a per relationship
- ### type basis, allowing us to flag outliers for each particular relationship
- ### type
- relstats = {}
- relCounts = {}
- outlierFiles = {}
- for relCode, relInfo in REL_LOOKUP.items():
- relName, relColor, relStyle = relInfo
- useme = [means[x] for x in xrange(len(means)) if rels[x] == relCode]
- relCounts[relCode] = len(useme)
- mm = scipy.mean(useme)
- ms = scipy.std(useme)
- useme = [sdevs[x] for x in xrange(len(sdevs)) if rels[x] == relCode]
- sm = scipy.mean(useme)
- ss = scipy.std(useme)
- relstats[relCode] = {'sd':(sm,ss), 'mean':(mm,ms)}
- logf.write('Relstate %s: mean(mean)=%3.2f sdev(mean)=%3.2f, mean(sdev)=%3.2f sdev(sdev)=%3.2f\n' % (relName, mm, ms, sm, ss))
-
- ### now fake z scores for each subject like abecasis recommends max(|zmu|,|zsd|)
- ### within each group, for each pair, z=(groupmean-pairmean)/groupsd
- available = len(means)
- logf.write('%d pairs are available of %d\n' % (available, tot))
- ### s = '\nOutliers:\nrelationship\tzmean\tzsd\tped1\tped2\tmean\tsd\trmeanmean\trmeansd\trsdmean\trsdsd\n'
- ### logf.write(s)
- pairnum = 0
- offset = 0
- nOutliers = 0
- cexs = []
- outlierRecords = dict([(r, []) for r in range(N_RELATIONSHIP_TYPES)])
- zsdmax = 0
- for s1 in range(nSubjects):
- if s1 in emptyRows:
- continue
- (fid1,iid1,did1,mid1,sex1,aff1,ok1,d_sid1,m_sid1) = scache[s1]
- for s2 in range(s1+1, nSubjects):
- if s2 in emptyRows:
- continue
- if pairnum not in skip:
- ### Get group stats for this relationship
- (fid2,iid2,did2,mid2,sex2,aff2,ok2,d_sid2,m_sid2) = scache[s2]
- try:
- r = rels[offset]
- except IndexError:
- logf.write('###OOPS offset %d available %d pairnum %d len(rels) %d', offset, available, pairnum, len(rels))
- rmm,rmd = relstats[r]['mean'] # group mean, group meansd alleles shared
- rdm,rdd = relstats[r]['sd'] # group sdmean, group sdsd alleles shared
-
- try:
- zsd = (sdevs[offset] - rdm)/rdd # distance from group mean in group sd units
- except:
- zsd = 1
- if abs(zsd) > zsdmax:
- zsdmax = zsd # keep for sort scaling
- try:
- zmean = (means[offset] - rmm)/rmd # distance from group mean
- except:
- zmean = 1
- zmeans[offset] = zmean
- zstds[offset] = zsd
- pid=(s1,s2)
- zrad = max(zsd,zmean)
- if zrad < 4:
- zrad = 2
- elif 4 < zrad < 15:
- zrad = 3 # to 9
- else: # > 15 6=24+
- zrad=zrad/4
- zrad = min(zrad,6) # scale limit
- zrad = max(2,max(zsd,zmean)) # as > 2, z grows
- pair_data[pid] = (zmean,zsd,r,zrad)
- if max(zsd,zmean) > Zcutoff: # is potentially interesting
- mean = means[offset]
- sdev = sdevs[offset]
- outlierRecords[r].append((mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd))
- nOutliers += 1
- tbl.write('%s_%s\t%s_%s\t%f\t%f\t%f\t%f\t%d\t%s\n' % \
- (fid1, iid1, fid2, iid2, mean, sdev, zmean,zsd, ngeno, relcode))
- offset += 1
- pairnum += 1
- logf.write( 'Outliers: %s\n' % (nOutliers))
-
- ### Write outlier files for each relationship type
- repOut.append('<h2>Outliers in tab delimited files linked above are also listed below</h2>')
- lzsd = round(numpy.log10(zsdmax)) + 1
- scalefactor = 10**lzsd
- for relCode, relInfo in REL_LOOKUP.items():
- relName, _, _ = relInfo
- outliers = outlierRecords[relCode]
- if not outliers:
- continue
- outliers = [(scalefactor*int(abs(x[3]))+ int(abs(x[2])),x) for x in outliers] # decorate
- outliers.sort()
- logf.write('### outliers after decorated sort=%s' % outliers)
- outliers.reverse() # largest deviation first
- logf.write('### outliers after decorated sort=%s' % outliers)
- outliers = [x[1] for x in outliers] # undecorate
- nrows = len(outliers)
- truncated = 0
- if nrows > MAX_SHOW_ROWS:
- s = '<h3>%s outlying pairs (top %d of %d) from %s</h3><table border="0" cellpadding="3">' % (relName,
- MAX_SHOW_ROWS,nrows,title)
- truncated = nrows - MAX_SHOW_ROWS
- else:
- s = '<h3>%s outlying pairs (n=%d) from %s</h3><table border="0" cellpadding="3">' % (relName,nrows,title)
- repOut.append(s)
- fhname = '%s_rgGRR_%s_outliers.xls' % (title, relName)
- fhpath = os.path.join(outdir,fhname)
- fh = open(fhpath, 'w')
- newfiles.append(fhname)
- explanations.append('%s Outlier Pairs %s, N=%d, Cutoff SD=%f' % (relName,title,len(outliers),Zcutoff))
- fh.write(OUTLIERS_HEADER)
- s = ''.join(['<th>%s</th>' % x for x in OUTLIERS_HEADER_list])
- repOut.append('<tr align="center">%s</tr>' % s)
- for n,rec in enumerate(outliers):
- #(mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd) = rec
- fh.write('%f\t%f\t%f\t%f\t%s\t%s\t%s\t%s\t%f\t%f\t%f\t%f\n' % tuple(rec))
- # (mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd))
- s = '''<td>%f</td><td>%f</td><td>%f</td><td>%f</td><td>%s</td><td>%s</td>
- <td>%s</td><td>%s</td><td>%f</td><td>%f</td><td>%f</td><td>%f</td>''' % tuple(rec)
- if n < MAX_SHOW_ROWS:
- repOut.append('<tr align="center">%s</tr>' % s)
- if truncated > 0:
- repOut.append('<H2>WARNING: %d rows truncated - see outlier file for all %d rows</H2>' % (truncated,
- nrows))
- fh.close()
- repOut.append('</table><p>')
-
- ### Now, draw the plot in jpeg and svg formats, and optionally in the PDF format
- ### if requested
- logf.write('Plotting ...')
- pointColors = [REL_COLORS[rel] for rel in rels]
- pointStyles = [REL_POINTS[rel] for rel in rels]
-
- mainTitle = '%s (%s subjects, %d snp)' % (title, nSubjects, nrsSamples)
- svg.write(SVG_HEADER % (SVG_COLORS[0],SVG_COLORS[1],SVG_COLORS[2],SVG_COLORS[3],SVG_COLORS[4],
- SVG_COLORS[5],SVG_COLORS[6],SVG_COLORS[0],SVG_COLORS[0],SVG_COLORS[1],SVG_COLORS[1],
- SVG_COLORS[2],SVG_COLORS[2],SVG_COLORS[3],SVG_COLORS[3],SVG_COLORS[4],SVG_COLORS[4],
- SVG_COLORS[5],SVG_COLORS[5],SVG_COLORS[6],SVG_COLORS[6],mainTitle))
- #rpy.r.jpeg(filename='%s.jpg' % (title), width=1600, height=1200, pointsize=12, quality=100, bg='white')
- #rpy.r.par(mai=(1,1,1,0.5))
- #rpy.r('par(xaxs="i",yaxs="i")')
- #rpy.r.plot(means, sdevs, main=mainTitle, ylab=Y_AXIS_LABEL, xlab=X_AXIS_LABEL, cex=cexs, col=pointColors, pch=pointStyles, xlim=(0,2), ylim=(0,2))
- #rpy.r.legend(LEGEND_ALIGN, legend=REL_STATES, pch=REL_POINTS, col=REL_COLORS, title=LEGEND_TITLE)
- #rpy.r.grid(nx=10, ny=10, col='lightgray', lty='dotted')
- #rpy.r.dev_off()
-
- ### We will now go through each relationship type to partition plot points
- ### into "bulk" and "outlier" groups. Bulk points will represent common
- ### mean/sdev pairs and will cover the majority of the points in the plot --
- ### they will use generic tooltip informtion about all of the pairs
- ### represented by that point. "Outlier" points will be uncommon pairs,
- ### with very specific information in their tooltips. It would be nice to
- ### keep hte total number of plotted points in the SVG representation to
- ### ~10000 (certainly less than 100000?)
- pointMap = {}
- orderedRels = [y[1] for y in reversed(sorted([(relCounts.get(x, 0),x) for x in REL_LOOKUP.keys()]))]
- # do we really want this? I want out of zone points last and big
- for relCode in orderedRels:
- svgColor = SVG_COLORS[relCode]
- relName, relColor, relStyle = REL_LOOKUP[relCode]
- svg.write('<g id="%s" style="stroke:%s; fill:%s; fill-opacity:1.0; stroke-width:1;" cursor="pointer">\n' % (relName, svgColor, svgColor))
- pMap = pointMap.setdefault(relCode, {})
- nPoints = 0
- rpairs=[]
- rgenos=[]
- rmeans=[]
- rsdevs=[]
- rz = []
- for x,rel in enumerate(rels): # all pairs
- if rel == relCode:
- s1,s2 = pairs[x]
- pid=(s1,s2)
- zmean,zsd,r,zrad = pair_data[pid][:4]
- rpairs.append(pairs[x])
- rgenos.append(ngenoL[x])
- rmeans.append(means[x])
- rsdevs.append(sdevs[x])
- rz.append(zrad)
- ### Now add the svg point group for this relationship to the svg file
- for x in range(len(rmeans)):
- svgX = '%d' % ((rmeans[x] - 1.0) * PLOT_WIDTH) # changed so mean scale is 1-2
- svgY = '%d' % (PLOT_HEIGHT - (rsdevs[x] * PLOT_HEIGHT)) # changed so sd scale is 0-1
- s1, s2 = rpairs[x]
- (fid1,uid1,did1,mid1,sex1,phe1,iid1,d_sid1,m_sid1) = scache[s1]
- (fid2,uid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache[s2]
- ngenos = rgenos[x]
- nPoints += 1
- point = pMap.setdefault((svgX, svgY), [])
- point.append((rmeans[x], rsdevs[x], fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, ngenos,rz[x]))
- for (svgX, svgY) in pMap:
- points = pMap[(svgX, svgY)]
- svgX = int(svgX)
- svgY = int(svgY)
- if len(points) > 1:
- mmean,dmean = calcMeanSD([p[0] for p in points])
- msdev,dsdev = calcMeanSD([p[1] for p in points])
- mgeno,dgeno = calcMeanSD([p[-1] for p in points])
- mingeno = min([p[-1] for p in points])
- maxgeno = max([p[-1] for p in points])
- svg.write("""<circle cx="%d" cy="%d" r="2"
- onmouseover="showBTT(evt, %d, %1.2f, %1.2f, %1.2f, %1.2f, %d, %d, %d, %d, %d)"
- onmouseout="hideBTT(evt)" />\n""" % (svgX, svgY, relCode, mmean, dmean, msdev, dsdev, len(points), mgeno, dgeno, mingeno, maxgeno))
- else:
- mean, sdev, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, ngenos, zrad = points[0][:12]
- rmean = float(relstats[relCode]['mean'][0])
- rsdev = float(relstats[relCode]['sd'][0])
- if zrad < 4:
- zrad = 2
- elif 4 < zrad < 9:
- zrad = 3 # to 9
- else: # > 9 5=15+
- zrad=zrad/3
- zrad = min(zrad,5) # scale limit
- if zrad <= 3:
- svg.write('<circle cx="%d" cy="%d" r="%s" onmouseover="showOTT(evt, %d, \'%s,%s,%s,%s\', \'%s,%s,%s,%s\', %1.2f, %1.2f, %s, %1.2f, %1.2f)" onmouseout="hideOTT(evt)" />\n' % (svgX, svgY, zrad, relCode, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, mean, sdev, ngenos, rmean, rsdev))
- else: # highlight pairs a long way from expectation by outlining circle in red
- svg.write("""<circle cx="%d" cy="%d" r="%s" style="stroke:red; fill:%s; fill-opacity:1.0; stroke-width:1;"
- onmouseover="showOTT(evt, %d, \'%s,%s,%s,%s\', \'%s,%s,%s,%s\', %1.2f, %1.2f, %s, %1.2f, %1.2f)"
- onmouseout="hideOTT(evt)" />\n""" % \
- (svgX, svgY, zrad, svgColor, relCode, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, mean, sdev, ngenos, rmean, rsdev))
- svg.write('</g>\n')
-
- ### Create a pdf as well if indicated on the command line
- ### WARNING! for framingham share, with about 50M pairs, this is a 5.5GB pdf!
-## if pdftoo:
-## pdfname = '%s.pdf' % (title)
-## rpy.r.pdf(pdfname, 6, 6)
-## rpy.r.par(mai=(1,1,1,0.5))
-## rpy.r('par(xaxs="i",yaxs="i")')
-## rpy.r.plot(means, sdevs, main='%s, %d snp' % (title, nSamples), ylab=Y_AXIS_LABEL, xlab=X_AXIS_LABEL, cex=cexs, col=pointColors, pch=pointStyles, xlim=(0,2), ylim=(0,2))
-## rpy.r.legend(LEGEND_ALIGN, legend=REL_STATES, pch=REL_POINTS, col=REL_COLORS, title=LEGEND_TITLE)
-## rpy.r.grid(nx=10, ny=10, col='lightgray', lty='dotted')
-## rpy.r.dev_off()
-
- ### Draw polygons
- if showPolygons:
- svg.write('<g id="polygons" cursor="pointer">\n')
- for rel, poly in POLYGONS.items():
- points = ' '.join(['%s,%s' % ((p[0]-1.0)*float(PLOT_WIDTH), (PLOT_HEIGHT - p[1]*PLOT_HEIGHT)) for p in poly])
- svg.write('<polygon points="%s" fill="transparent" style="stroke:%s; stroke-width:1"/>\n' % (points, SVG_COLORS[rel]))
- svg.write('</g>\n')
-
-
- svg.write(SVG_FOOTER)
- svg.close()
- return newfiles,explanations,repOut
-
-def doIBS(n=100):
- """parse parameters from galaxy
- expect 'input pbed path' 'basename' 'outpath' 'title' 'logpath' 'n'
- <command interpreter="python">
- rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name"
- '$out_file1' '$out_file1.files_path' "$title" '$n' '$Z'
- </command>
-
- """
- u="""<command interpreter="python">
- rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name"
- '$out_file1' '$out_file1.files_path' "$title" '$n' '$Z'
- </command>"""
-
- if len(sys.argv) < 8:
- print >> sys.stdout, 'Need pbed inpath, basename, out_htmlname, outpath, title, logpath, nSNP, Zcutoff on command line please'
- print >> sys.stdout, u
- sys.exit(1)
- ts = '%s%s' % (string.punctuation,string.whitespace)
- ptran = string.maketrans(ts,'_'*len(ts))
- inpath = sys.argv[1]
- basename = sys.argv[2]
- outhtml = sys.argv[3]
- newfilepath = sys.argv[4]
- try:
- os.makedirs(newfilepath)
- except:
- pass
- title = sys.argv[5].translate(ptran)
- logfname = 'Log_%s.txt' % title
- logpath = os.path.join(newfilepath,logfname) # log was a child - make part of html extra_files_path zoo
- n = int(sys.argv[6])
- try:
- Zcutoff = float(sys.argv[7])
- except:
- Zcutoff = 2.0
- try:
- os.makedirs(newfilepath)
- except:
- pass
- logf = file(logpath,'w')
- newfiles,explanations,repOut = doIBSpy(inpath=inpath,basename=basename,outdir=newfilepath,
- logf=logf,nrsSamples=n,title=title,pdftoo=0,Zcutoff=Zcutoff)
- logf.close()
- logfs = file(logpath,'r').readlines()
- lf = file(outhtml,'w')
- lf.write(galhtmlprefix % PROGNAME)
- # this is a mess. todo clean up - should each datatype have it's own directory? Yes
- # probably. Then titles are universal - but userId libraries are separate.
- s = '<div>Output from %s run at %s<br>\n' % (PROGNAME,timenow())
- lf.write('<h4>%s</h4>\n' % s)
- fixed = ["'%s'" % x for x in sys.argv] # add quotes just in case
- s = 'If you need to rerun this analysis, the command line was\n<pre>%s</pre>\n</div>' % (' '.join(fixed))
- lf.write(s)
- #s = """<object data="%s" type="image/svg+xml" width="%d" height="%d">
- # <embed src="%s" type="image/svg+xml" width="%d" height="%d" />
- # </object>""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT,newfiles[0],PLOT_WIDTH,PLOT_HEIGHT)
- s = """ <embed src="%s" type="image/svg+xml" width="%d" height="%d" />""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT)
- #s = """ <iframe src="%s" type="image/svg+xml" width="%d" height="%d" />""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT)
- lf.write(s)
- lf.write('<div><h4>Click the links below to save output files and plots</h4><br><ol>\n')
- for i in range(len(newfiles)):
- if i == 0:
- lf.write('<li><a href="%s" type="image/svg+xml" >%s</a></li>\n' % (newfiles[i],explanations[i]))
- else:
- lf.write('<li><a href="%s">%s</a></li>\n' % (newfiles[i],explanations[i]))
- flist = os.listdir(newfilepath)
- for fname in flist:
- if not fname in newfiles:
- lf.write('<li><a href="%s">%s</a></li>\n' % (fname,fname))
- lf.write('</ol></div>')
- lf.write('<div>%s</div>' % ('\n'.join(repOut))) # repOut is a list of tables
- lf.write('<div><hr><h3>Log from this job (also stored in %s)</h3><pre>%s</pre><hr></div>' % (logfname,'\n'.join(logfs)))
- lf.write('</body></html>\n')
- lf.close()
- logf.close()
-
-if __name__ == '__main__':
- doIBS()
-
-
+"""
+# july 2009: Need to see outliers so need to draw them last?
+# could use clustering on the zscores to guess real relationships for unrelateds
+# but definitely need to draw last
+# added MAX_SHOW_ROWS to limit the length of the main report page
+# Changes for Galaxy integration
+# added more robust knuth method for one pass mean and sd
+# no difference really - let's use scipy.mean() and scipy.std() instead...
+# fixed labels and changed to .xls for outlier reports so can open in excel
+# interesting - with a few hundred subjects, 5k gives good resolution
+# and 100k gives better but not by much
+# TODO remove non autosomal markers
+# TODO it would be best if label had the zmean and zsd as these are what matter for
+# outliers rather than the group mean/sd
+# mods to rgGRR.py from channing CVS which John Ziniti has rewritten to produce SVG plots
+# to make a Galaxy tool - we need the table of mean and SD for interesting pairs, the SVG and the log
+# so the result should be an HTML file
+
+# rgIBS.py
+# use a random subset of markers for a quick ibs
+# to identify sample dups and closely related subjects
+# try snpMatrix and plink and see which one works best for us?
+# abecasis grr plots mean*sd for every subject to show clusters
+# mods june 23 rml to avoid non-autosomal markers
+# we seem to be distinguishing parent-child by gender - 2 clouds!
+
+
+snpMatrix from David Clayton has:
+ibs.stats function to calculate the identity-by-state stats of a group of samples
+Description
+Given a snp.matrix-class or a X.snp.matrix-class object with N samples, calculates some statistics
+about the relatedness of every pair of samples within.
+
+Usage
+ibs.stats(x)
+8 ibs.stats
+Arguments
+x a snp.matrix-class or a X.snp.matrix-class object containing N samples
+Details
+No-calls are excluded from consideration here.
+Value
+A data.frame containing N(N - 1)/2 rows, where the row names are the sample name pairs separated
+by a comma, and the columns are:
+Count count of identical calls, exclusing no-calls
+Fraction fraction of identical calls comparied to actual calls being made in both samples
+Warning
+In some applications, it may be preferable to subset a (random) selection of SNPs first - the
+calculation
+time increases as N(N - 1)M/2 . Typically for N = 800 samples and M = 3000 SNPs, the
+calculation time is about 1 minute. A full GWA scan could take hours, and quite unnecessary for
+simple applications such as checking for duplicate or related samples.
+Note
+This is mostly written to find mislabelled and/or duplicate samples.
+Illumina indexes their SNPs in alphabetical order so the mitochondria SNPs comes first - for most
+purpose it is undesirable to use these SNPs for IBS purposes.
+TODO: Worst-case S4 subsetting seems to make 2 copies of a large object, so one might want to
+subset before rbind(), etc; a future version of this routine may contain a built-in subsetting facility
+"""
+import sys,os,time,random,string,copy,optparse
+
+try:
+ set
+except NameError:
+ from Sets import Set as set
+
+from rgutils import timenow,pruneLD,plinke
+import plinkbinJZ
+
+
+opts = None
+verbose = False
+
+showPolygons = False
+
+class NullDevice:
+ def write(self, s):
+ pass
+
+tempstderr = sys.stderr # save
+sys.stderr = NullDevice()
+# need to avoid blather about deprecation and other strange stuff from scipy
+# the current galaxy job runner assumes that
+# the job is in error if anything appears on sys.stderr
+# grrrrr. James wants to keep it that way instead of using the
+# status flag for some strange reason. Presumably he doesn't use R or (in this case, scipy)
+import numpy
+import scipy
+from scipy import weave
+
+
+sys.stderr=tempstderr
+
+
+PROGNAME = os.path.split(sys.argv[0])[-1]
+X_AXIS_LABEL = 'Mean Alleles Shared'
+Y_AXIS_LABEL = 'SD Alleles Shared'
+LEGEND_ALIGN = 'topleft'
+LEGEND_TITLE = 'Relationship'
+DEFAULT_SYMBOL_SIZE = 1.0 # default symbol size
+DEFAULT_SYMBOL_SIZE = 0.5 # default symbol size
+
+### Some colors for R/rpy
+R_BLACK = 1
+R_RED = 2
+R_GREEN = 3
+R_BLUE = 4
+R_CYAN = 5
+R_PURPLE = 6
+R_YELLOW = 7
+R_GRAY = 8
+
+### ... and some point-styles
+
+###
+PLOT_HEIGHT = 600
+PLOT_WIDTH = 1150
+
+
+#SVG_COLORS = ('black', 'darkblue', 'blue', 'deepskyblue', 'firebrick','maroon','crimson')
+#SVG_COLORS = ('cyan','dodgerblue','mediumpurple', 'fuchsia', 'red','gold','gray')
+SVG_COLORS = ('cyan','dodgerblue','mediumpurple','forestgreen', 'lightgreen','gold','gray')
+# dupe,parentchild,sibpair,halfsib,parents,unrel,unkn
+#('orange', 'red', 'green', 'chartreuse', 'blue', 'purple', 'gray')
+
+OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Rel_Mean)\tSdev(Rel_Mean)\tMean(Rel_Sdev)\tSdev(Rel_Sdev)\n'
+OUTLIERS_HEADER_list = ['Mean','Sdev','ZMean','ZSdev','FID1','IID1','FID2','IID2',
+'RGMean_M','RGMean_SD','RGSD_M','RGSD_SD']
+TABLE_HEADER='fid1 iid1\tfid2 iid2\tmean\tsdev\tzmean\tzsdev\tgeno\trelcode\n'
+
+
+### Relationship codes, text, and lookups/mappings
+N_RELATIONSHIP_TYPES = 7
+REL_DUPE, REL_PARENTCHILD, REL_SIBS, REL_HALFSIBS, REL_RELATED, REL_UNRELATED, REL_UNKNOWN = range(N_RELATIONSHIP_TYPES)
+REL_LOOKUP = {
+ REL_DUPE: ('dupe', R_BLUE, 1),
+ REL_PARENTCHILD: ('parentchild', R_YELLOW, 1),
+ REL_SIBS: ('sibpairs', R_RED, 1),
+ REL_HALFSIBS: ('halfsibs', R_GREEN, 1),
+ REL_RELATED: ('parents', R_PURPLE, 1),
+ REL_UNRELATED: ('unrelated', R_CYAN, 1),
+ REL_UNKNOWN: ('unknown', R_GRAY, 1),
+ }
+OUTLIER_STDEVS = {
+ REL_DUPE: 2,
+ REL_PARENTCHILD: 2,
+ REL_SIBS: 2,
+ REL_HALFSIBS: 2,
+ REL_RELATED: 2,
+ REL_UNRELATED: 3,
+ REL_UNKNOWN: 2,
+ }
+# note now Z can be passed in
+
+REL_STATES = [REL_LOOKUP[r][0] for r in range(N_RELATIONSHIP_TYPES)]
+REL_COLORS = SVG_COLORS
+REL_POINTS = [REL_LOOKUP[r][2] for r in range(N_RELATIONSHIP_TYPES)]
+
+DEFAULT_MAX_SAMPLE_SIZE = 10000
+
+REF_COUNT_HOM1 = 3
+REF_COUNT_HET = 2
+REF_COUNT_HOM2 = 1
+MISSING = 0
+MAX_SHOW_ROWS = 100 # framingham has millions - delays showing output page - so truncate and explain
+MARKER_PAIRS_PER_SECOND_SLOW = 15000000.0
+MARKER_PAIRS_PER_SECOND_FAST = 70000000.0
+
+
+galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+"""
+
+
+SVG_HEADER = '''<?xml version="1.0" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.2//EN" "http://www.w3.org/Graphics/SVG/1.2/DTD/svg12.dtd">
+
+<svg width="1280" height="800"
+ xmlns="http://www.w3.org/2000/svg" version="1.2"
+ xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()">
+
+ <script type="text/ecmascript" xlink:href="/static/scripts/checkbox_and_radiobutton.js"/>
+ <script type="text/ecmascript" xlink:href="/static/scripts/helper_functions.js"/>
+ <script type="text/ecmascript" xlink:href="/static/scripts/timer.js"/>
+ <script type="text/ecmascript">
+ <![CDATA[
+ var checkBoxes = new Array();
+ var radioGroupBandwidth;
+ var colours = ['%s','%s','%s','%s','%s','%s','%s'];
+ function init() {
+ var style = {"font-family":"Arial,Helvetica", "fill":"black", "font-size":12};
+ var dist = 12;
+ var yOffset = 4;
+
+ //A checkBox for each relationship type dupe,parentchild,sibpair,halfsib,parents,unrel,unkn
+ checkBoxes["dupe"] = new checkBox("dupe","checkboxes",20,40,"cbRect","cbCross",true,"Duplicate",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["parentchild"] = new checkBox("parentchild","checkboxes",20,60,"cbRect","cbCross",true,"Parent-Child",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["sibpairs"] = new checkBox("sibpairs","checkboxes",20,80,"cbRect","cbCross",true,"Sib-pairs",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["halfsibs"] = new checkBox("halfsibs","checkboxes",20,100,"cbRect","cbCross",true,"Half-sibs",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["parents"] = new checkBox("parents","checkboxes",20,120,"cbRect","cbCross",true,"Parents",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["unrelated"] = new checkBox("unrelated","checkboxes",20,140,"cbRect","cbCross",true,"Unrelated",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["unknown"] = new checkBox("unknown","checkboxes",20,160,"cbRect","cbCross",true,"Unknown",style,dist,yOffset,undefined,hideShowLayer);
+
+ }
+
+ function hideShowLayer(id, status, label) {
+ var vis = "hidden";
+ if (status) {
+ vis = "visible";
+ }
+ document.getElementById(id).setAttributeNS(null, 'visibility', vis);
+ }
+
+ function showBTT(evt, rel, mm, dm, md, dd, n, mg, dg, lg, hg) {
+ var x = parseInt(evt.pageX)-250;
+ var y = parseInt(evt.pageY)-110;
+ switch(rel) {
+ case 0:
+ fill = colours[rel];
+ relt = "dupe";
+ break;
+ case 1:
+ fill = colours[rel];
+ relt = "parentchild";
+ break;
+ case 2:
+ fill = colours[rel];
+ relt = "sibpairs";
+ break;
+ case 3:
+ fill = colours[rel];
+ relt = "halfsibs";
+ break;
+ case 4:
+ fill = colours[rel];
+ relt = "parents";
+ break;
+ case 5:
+ fill = colours[rel];
+ relt = "unrelated";
+ break;
+ case 6:
+ fill = colours[rel];
+ relt = "unknown";
+ break;
+ default:
+ fill = "cyan";
+ relt = "ERROR_CODE: "+rel;
+ }
+
+ document.getElementById("btRel").textContent = "GROUP: "+relt;
+ document.getElementById("btMean").textContent = "mean="+mm+" +/- "+dm;
+ document.getElementById("btSdev").textContent = "sdev="+dm+" +/- "+dd;
+ document.getElementById("btPair").textContent = "npairs="+n;
+ document.getElementById("btGeno").textContent = "ngenos="+mg+" +/- "+dg+" (min="+lg+", max="+hg+")";
+ document.getElementById("btHead").setAttribute('fill', fill);
+
+ var tt = document.getElementById("btTip");
+ tt.setAttribute("transform", "translate("+x+","+y+")");
+ tt.setAttribute('visibility', 'visible');
+ }
+
+ function showOTT(evt, rel, s1, s2, mean, sdev, ngeno, rmean, rsdev) {
+ var x = parseInt(evt.pageX)-150;
+ var y = parseInt(evt.pageY)-180;
+
+ switch(rel) {
+ case 0:
+ fill = colours[rel];
+ relt = "dupe";
+ break;
+ case 1:
+ fill = colours[rel];
+ relt = "parentchild";
+ break;
+ case 2:
+ fill = colours[rel];
+ relt = "sibpairs";
+ break;
+ case 3:
+ fill = colours[rel];
+ relt = "halfsibs";
+ break;
+ case 4:
+ fill = colours[rel];
+ relt = "parents";
+ break;
+ case 5:
+ fill = colours[rel];
+ relt = "unrelated";
+ break;
+ case 6:
+ fill = colours[rel];
+ relt = "unknown";
+ break;
+ default:
+ fill = "cyan";
+ relt = "ERROR_CODE: "+rel;
+ }
+
+ document.getElementById("otRel").textContent = "PAIR: "+relt;
+ document.getElementById("otS1").textContent = "s1="+s1;
+ document.getElementById("otS2").textContent = "s2="+s2;
+ document.getElementById("otMean").textContent = "mean="+mean;
+ document.getElementById("otSdev").textContent = "sdev="+sdev;
+ document.getElementById("otGeno").textContent = "ngenos="+ngeno;
+ document.getElementById("otRmean").textContent = "relmean="+rmean;
+ document.getElementById("otRsdev").textContent = "relsdev="+rsdev;
+ document.getElementById("otHead").setAttribute('fill', fill);
+
+ var tt = document.getElementById("otTip");
+ tt.setAttribute("transform", "translate("+x+","+y+")");
+ tt.setAttribute('visibility', 'visible');
+ }
+
+ function hideBTT(evt) {
+ document.getElementById("btTip").setAttributeNS(null, 'visibility', 'hidden');
+ }
+
+ function hideOTT(evt) {
+ document.getElementById("otTip").setAttributeNS(null, 'visibility', 'hidden');
+ }
+
+ ]]>
+ </script>
+ <defs>
+ <!-- symbols for check boxes -->
+ <symbol id="cbRect" overflow="visible">
+ <rect x="-5" y="-5" width="10" height="10" fill="white" stroke="dimgray" stroke-width="1" cursor="pointer"/>
+ </symbol>
+ <symbol id="cbCross" overflow="visible">
+ <g pointer-events="none" stroke="black" stroke-width="1">
+ <line x1="-3" y1="-3" x2="3" y2="3"/>
+ <line x1="3" y1="-3" x2="-3" y2="3"/>
+ </g>
+ </symbol>
+ </defs>
+
+<desc>Developer Works Dynamic Scatter Graph Scaling Example</desc>
+
+<!-- Now Draw the main X and Y axis -->
+<g style="stroke-width:1.0; stroke:black; shape-rendering:crispEdges">
+ <!-- X Axis top and bottom -->
+ <path d="M 100 100 L 1250 100 Z"/>
+ <path d="M 100 700 L 1250 700 Z"/>
+
+ <!-- Y Axis left and right -->
+ <path d="M 100 100 L 100 700 Z"/>
+ <path d="M 1250 100 L 1250 700 Z"/>
+</g>
+
+<g transform="translate(100,100)">
+
+ <!-- Grid Lines -->
+ <g style="fill:none; stroke:#dddddd; stroke-width:1; stroke-dasharray:2,2; text-anchor:end; shape-rendering:crispEdges">
+
+ <!-- Vertical grid lines -->
+ <line x1="125" y1="0" x2="115" y2="600" />
+ <line x1="230" y1="0" x2="230" y2="600" />
+ <line x1="345" y1="0" x2="345" y2="600" />
+ <line x1="460" y1="0" x2="460" y2="600" />
+ <line x1="575" y1="0" x2="575" y2="600" style="stroke-dasharray:none;" />
+ <line x1="690" y1="0" x2="690" y2="600" />
+ <line x1="805" y1="0" x2="805" y2="600" />
+ <line x1="920" y1="0" x2="920" y2="600" />
+ <line x1="1035" y1="0" x2="1035" y2="600" />
+
+ <!-- Horizontal grid lines -->
+ <line x1="0" y1="60" x2="1150" y2="60" />
+ <line x1="0" y1="120" x2="1150" y2="120" />
+ <line x1="0" y1="180" x2="1150" y2="180" />
+ <line x1="0" y1="240" x2="1150" y2="240" />
+ <line x1="0" y1="300" x2="1150" y2="300" style="stroke-dasharray:none;" />
+ <line x1="0" y1="360" x2="1150" y2="360" />
+ <line x1="0" y1="420" x2="1150" y2="420" />
+ <line x1="0" y1="480" x2="1150" y2="480" />
+ <line x1="0" y1="540" x2="1150" y2="540" />
+ </g>
+
+ <!-- Legend -->
+ <g style="fill:black; stroke:none" font-size="12" font-family="Arial" transform="translate(25,25)">
+ <rect width="160" height="270" style="fill:none; stroke:black; shape-rendering:crispEdges" />
+ <text x="5" y="20" style="fill:black; stroke:none;" font-size="13" font-weight="bold">Given Pair Relationship</text>
+ <rect x="120" y="35" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="55" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="75" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="95" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="115" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="135" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="155" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/>
+ <text x="15" y="195" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore gt 15</text>
+ <circle cx="125" cy="192" r="6" style="stroke:red; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
+ <text x="15" y="215" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore 4 to 15</text>
+ <circle cx="125" cy="212" r="3" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
+ <text x="15" y="235" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore lt 4</text>
+ <circle cx="125" cy="232" r="2" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
+ <g id="checkboxes">
+ </g>
+ </g>
+
+
+ <g style='fill:black; stroke:none' font-size="17" font-family="Arial">
+ <!-- X Axis Labels -->
+ <text x="480" y="660">Mean Alleles Shared</text>
+ <text x="0" y="630" >1.0</text>
+ <text x="277" y="630" >1.25</text>
+ <text x="564" y="630" >1.5</text>
+ <text x="842" y="630" >1.75</text>
+ <text x="1140" y="630" >2.0</text>
+ </g>
+
+ <g transform="rotate(270)" style="fill:black; stroke:none" font-size="17" font-family="Arial">
+ <!-- Y Axis Labels -->
+ <text x="-350" y="-40">SD Alleles Shared</text>
+ <text x="-20" y="-10" >1.0</text>
+ <text x="-165" y="-10" >0.75</text>
+ <text x="-310" y="-10" >0.5</text>
+ <text x="-455" y="-10" >0.25</text>
+ <text x="-600" y="-10" >0.0</text>
+ </g>
+
+<!-- Plot Title -->
+<g style="fill:black; stroke:none" font-size="18" font-family="Arial">
+ <text x="425" y="-30">%s</text>
+</g>
+
+<!-- One group/layer of points for each relationship type -->
+'''
+
+SVG_FOOTER = '''
+<!-- End of Data -->
+</g>
+<g id="btTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial">
+ <rect width="250" height="110" style="fill:silver" rx="2" ry="2"/>
+ <rect id="btHead" width="250" height="20" rx="2" ry="2" />
+ <text id="btRel" y="14" x="85">unrelated</text>
+ <text id="btMean" y="40" x="4">mean=1.5 +/- 0.04</text>
+ <text id="btSdev" y="60" x="4">sdev=0.7 +/- 0.03</text>
+ <text id="btPair" y="80" x="4">npairs=1152</text>
+ <text id="btGeno" y="100" x="4">ngenos=4783 +/- 24 (min=1000, max=5000)</text>
+</g>
+
+<g id="otTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial">
+ <rect width="150" height="180" style="fill:silver" rx="2" ry="2"/>
+ <rect id="otHead" width="150" height="20" rx="2" ry="2" />
+ <text id="otRel" y="14" x="40">sibpairs</text>
+ <text id="otS1" y="40" x="4">s1=fid1,iid1</text>
+ <text id="otS2" y="60" x="4">s2=fid2,iid2</text>
+ <text id="otMean" y="80" x="4">mean=1.82</text>
+ <text id="otSdev" y="100" x="4">sdev=0.7</text>
+ <text id="otGeno" y="120" x="4">ngeno=4487</text>
+ <text id="otRmean" y="140" x="4">relmean=1.85</text>
+ <text id="otRsdev" y="160" x="4">relsdev=0.65</text>
+</g>
+</svg>
+'''
+
+OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Mean)\tSdev(Mean)\tMean(Sdev)\tSdev(Sdev)\n'
+
+DEFAULT_MAX_SAMPLE_SIZE = 5000
+
+REF_COUNT_HOM1 = 3
+REF_COUNT_HET = 2
+REF_COUNT_HOM2 = 1
+MISSING = 0
+
+MARKER_PAIRS_PER_SECOND_SLOW = 15000000
+MARKER_PAIRS_PER_SECOND_FAST = 70000000
+
+POLYGONS = {
+ REL_UNRELATED: ((1.360, 0.655), (1.385, 0.730), (1.620, 0.575), (1.610, 0.505)),
+ REL_HALFSIBS: ((1.630, 0.500), (1.630, 0.550), (1.648, 0.540), (1.648, 0.490)),
+ REL_SIBS: ((1.660, 0.510), (1.665, 0.560), (1.820, 0.410), (1.820, 0.390)),
+ REL_PARENTCHILD: ((1.650, 0.470), (1.650, 0.490), (1.750, 0.440), (1.750, 0.420)),
+ REL_DUPE: ((1.970, 0.000), (1.970, 0.150), (2.000, 0.150), (2.000, 0.000)),
+ }
+
+def distance(point1, point2):
+ """ Calculate the distance between two points
+ """
+ (x1,y1) = [float(d) for d in point1]
+ (x2,y2) = [float(d) for d in point2]
+ dx = abs(x1 - x2)
+ dy = abs(y1 - y2)
+ return math.sqrt(dx**2 + dy**2)
+
+def point_inside_polygon(x, y, poly):
+ """ Determine if a point (x,y) is inside a given polygon or not
+ poly is a list of (x,y) pairs.
+
+ Taken from: http://www.ariel.com.au/a/python-point-int-poly.html
+ """
+
+ n = len(poly)
+ inside = False
+
+ p1x,p1y = poly[0]
+ for i in range(n+1):
+ p2x,p2y = poly[i % n]
+ if y > min(p1y,p2y):
+ if y <= max(p1y,p2y):
+ if x <= max(p1x,p2x):
+ if p1y != p2y:
+ xinters = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x
+ if p1x == p2x or x <= xinters:
+ inside = not inside
+ p1x,p1y = p2x,p2y
+ return inside
+
+def readMap(pedfile):
+ """
+ """
+ mapfile = pedfile.replace('.ped', '.map')
+ marker_list = []
+ if os.path.exists(mapfile):
+ print 'readMap: %s' % (mapfile)
+ fh = file(mapfile, 'r')
+ for line in fh:
+ marker_list.append(line.strip().split())
+ fh.close()
+ print 'readMap: %s markers' % (len(marker_list))
+ return marker_list
+
+def calcMeanSD(useme):
+ """
+ A numerically stable algorithm is given below. It also computes the mean.
+ This algorithm is due to Knuth,[1] who cites Welford.[2]
+ n = 0
+ mean = 0
+ M2 = 0
+
+ foreach x in data:
+ n = n + 1
+ delta = x - mean
+ mean = mean + delta/n
+ M2 = M2 + delta*(x - mean) // This expression uses the new value of mean
+ end for
+
+ variance_n = M2/n
+ variance = M2/(n - 1)
+ """
+ mean = 0.0
+ M2 = 0.0
+ sd = 0.0
+ n = len(useme)
+ if n > 1:
+ for i,x in enumerate(useme):
+ delta = x - mean
+ mean = mean + delta/(i+1) # knuth uses n+=1 at start
+ M2 = M2 + delta*(x - mean) # This expression uses the new value of mean
+ variance = M2/(n-1) # assume is sample so lose 1 DOF
+ sd = pow(variance,0.5)
+ return mean,sd
+
+
+def doIBSpy(ped=None,basename='',outdir=None,logf=None,
+ nrsSamples=10000,title='title',pdftoo=0,Zcutoff=2.0):
+ #def doIBS(pedName, title, nrsSamples=None, pdftoo=False):
+ """ started with snpmatrix but GRR uses actual IBS counts and sd's
+ """
+ repOut = [] # text strings to add to the html display
+ refallele = {}
+ tblf = '%s_table.xls' % (title)
+ tbl = file(os.path.join(outdir,tblf), 'w')
+ tbl.write(TABLE_HEADER)
+ svgf = '%s.svg' % (title)
+ svg = file(os.path.join(outdir,svgf), 'w')
+
+ nMarkers = len(ped._markers)
+ if nMarkers < 5:
+ print sys.stderr, '### ERROR - %d is too few markers for reliable estimation in %s - terminating' % (nMarkers,PROGNAME)
+ sys.exit(1)
+ nSubjects = len(ped._subjects)
+ nrsSamples = min(nMarkers, nrsSamples)
+ if opts and opts.use_mito:
+ markers = range(nMarkers)
+ nrsSamples = min(len(markers), nrsSamples)
+ sampleIndexes = sorted(random.sample(markers, nrsSamples))
+ else:
+ autosomals = ped.autosomal_indices()
+ nrsSamples = min(len(autosomals), nrsSamples)
+ sampleIndexes = sorted(random.sample(autosomals, nrsSamples))
+
+ print ''
+ print 'Getting random.sample of %s from %s total' % (nrsSamples, nMarkers)
+ npairs = (nSubjects*(nSubjects-1))/2 # total rows in table
+ newfiles=[svgf,tblf]
+ explanations = ['rgGRR Plot (requires SVG)','Mean by SD alleles shared - %d rows' % npairs]
+ # these go with the output file links in the html file
+ s = 'Reading genotypes for %s subjects and %s markers\n' % (nSubjects, nrsSamples)
+ logf.write(s)
+ minUsegenos = nrsSamples/2 # must have half?
+ nGenotypes = nSubjects*nrsSamples
+ stime = time.time()
+ emptyRows = set()
+ genos = numpy.zeros((nSubjects, nrsSamples), dtype=int)
+ for s in xrange(nSubjects):
+ nValid = 0
+ #getGenotypesByIndices(self, s, mlist, format)
+ genos[s] = ped.getGenotypesByIndices(s, sampleIndexes, format='ref')
+ nValid = sum([1 for g in genos[s] if g])
+ if not nValid:
+ emptyRows.add(s)
+ sub = ped.getSubject(s)
+ print 'All missing for row %d (%s)' % (s, sub)
+ logf.write('All missing for row %d (%s)\n' % (s, sub))
+ rtime = time.time() - stime
+ if verbose:
+ print '@@Read %s genotypes in %s seconds' % (nGenotypes, rtime)
+
+
+ ### Now the expensive part. For each pair of subjects, we get the mean number
+ ### and standard deviation of shared alleles over all of the markers where both
+ ### subjects have a known genotype. Identical subjects should have mean shared
+ ### alleles very close to 2.0 with a standard deviation very close to 0.0.
+ tot = nSubjects*(nSubjects-1)/2
+ nprog = tot/10
+ nMarkerpairs = tot * nrsSamples
+ estimatedTimeSlow = nMarkerpairs/MARKER_PAIRS_PER_SECOND_SLOW
+ estimatedTimeFast = nMarkerpairs/MARKER_PAIRS_PER_SECOND_FAST
+
+ pairs = []
+ pair_data = {}
+ means = [] ## Mean IBS for each pair
+ ngenoL = [] ## Count of comparable genotypes for each pair
+ sdevs = [] ## Standard dev for each pair
+ rels = [] ## A relationship code for each pair
+ zmeans = [0.0 for x in xrange(tot)] ## zmean score for each pair for the relgroup
+ zstds = [0.0 for x in xrange(tot)] ## zstd score for each pair for the relgrp
+ skip = set()
+ ndone = 0 ## How many have been done so far
+
+ logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog))
+ logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow))
+
+ t1sum = 0
+ t2sum = 0
+ t3sum = 0
+ now = time.time()
+ scache = {}
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