--- a/tornado-plots/index.html Thu Nov 02 00:16:56 2023 -0400
+++ b/tornado-plots/index.html Sun Nov 05 12:37:35 2023 -0500
@@ -9,14 +9,16 @@
<body>
<main>
</main>
- <p>The graph is 100kb wide.</p>
+ <p>The graph is 100kb wide. The histogram is frequency of reads.</p>
<ul>
<li><b>cells:</b> number of cells in the population.</li>
<li><b>synthesis time:</b> simulated synthesis time (seconds).</li>
- <li><b>firing model:</b> whether to simulate exponential firing (uses firing half-life), or linear firing (uses firing probability).</li>
- <li><b>firing half-life:</b> the half-life of the origin with respect to firing (seconds), e.g. a value of 5 means that this origin will fire in half of the cells after 5 seconds. Only used when exponential firing is selected.</li>
- <li><b>firing probability:</b> the probability this origin will fire each second. Only used when linear firing is selected.</li>
+ <!-- <li><b>firing model:</b> whether to simulate exponential firing (uses firing half-life), or linear firing (uses firing probability).</li> -->
+ <!-- <li><b>firing half-life:</b> the half-life of the origin with respect to firing (seconds), e.g. a value of 5 means that this origin will fire in half of the cells after 5 seconds. Only used when exponential firing is selected.</li> -->
+ <li><b>firing probability:</b> the probability this origin will fire each second.
+ <!-- Only used when linear firing is selected. -->
+ </li>
<li><b>ori:</b> position of the origin.</li>
<li><b>left/right fork rates:</b> how fast each fork progresses (nt/second).</li>
<li><b>rate noise:</b> how much noise to add to each fork's rate (per fork, proportion of total rate).</li>
--- a/tornado-plots/sketch.js Thu Nov 02 00:16:56 2023 -0400
+++ b/tornado-plots/sketch.js Sun Nov 05 12:37:35 2023 -0500
@@ -34,7 +34,7 @@
function computeReadTimesExponential() {
let result = new Array();
n = _population.value();
- hl = _halfLife.value();
+ // hl = _halfLife.value();
sec = _seconds.value();
under = _undercutRate.value();
ts = 0.05;
@@ -135,11 +135,11 @@
seconds = _seconds.value();
overcutRate = _overcutRate.value();
overcutExpt = _overcutExpt.value();
- if (_firingModel.value() == 'e') {
- times = computeReadTimesExponential();
- } else if (_firingModel.value() == 'l') {
+ // if (_firingModel.value() == 'e') {
+ // times = computeReadTimesExponential();
+ // } else if (_firingModel.value() == 'l') {
times = computeReadTimesLinear();
- }
+ // }
_numReads.html(times.length + " reads");
for (i = 0; i < times.length; i++) {
@@ -203,7 +203,7 @@
function computeReadCount() {
pop = _population.value();
sec = _seconds.value();
- hl = _halfLife.value();
+ // hl = _halfLife.value();
under = _undercutRate.value();
// N(t) = N₀(1/2)^(t/hl)
@@ -308,16 +308,16 @@
_seconds = makeSlider("synthesis time", x, y, 0, 30, 10); y += 20;
- y += 10;
- _firingModel = createRadio();
- _firingModel.option('e', 'exponential firing');
- _firingModel.option('l', 'linear firing');
- _firingModel.position(x, y);
- _firingModel.size(400);
- _firingModel.selected('e');
- _firingModel.input(rerender);
- y += 20;
- _halfLife = makeSlider("firing half-life", x, y, 0.0, 30, 5); y += 20;
+ // y += 10;
+ // _firingModel = createRadio();
+ // _firingModel.option('e', 'exponential firing');
+ // _firingModel.option('l', 'linear firing');
+ // _firingModel.position(x, y);
+ // _firingModel.size(400);
+ // _firingModel.selected('e');
+ // _firingModel.input(rerender);
+ // y += 20;
+ // _halfLife = makeSlider("firing half-life", x, y, 0.0, 30, 5); y += 20;
_firingProb = makeSlider("firing probability", x, y, 0, 1, 0.1); y += 20;
_ori = makeSlider("ori", x, y, 0, _genomeLength, _genomeLength / 2); y += 20;
_lRate = makeSlider("left fork rate", x, y, 0, 10000, 2000); y += 20;