\n",
...
"source": [
"# Section 1. Introduction\n",
"\n",
"No code for this section.\n",
"\n",
"# Section 2. FRETBursts Overview\n",
"\n",
"No code for this section.\n",
"\n",
"# Section 3. Architecture and Concepts\n",
"\n",
"## 3.1 Photon Streams\n",
"\n",
"No code of figures in this section.\n",
"\n",
"## 3.2 Background Definitions\n",
"\n",
"For the paper's "To reproduce **Fig. 2 & 3** see the notebook:\n",
"\n",
"- [Figures - Background plots](Figures - Background plots.ipynb)\n",
"\n",
"## 3.3 The Data Class\n",
"\n",
"No code for this section.\n",
"\n",
"## 3.4 Introduction to Burst Search\n",
"\n",
"No code for this section.\n",
"\n",
"## 3.5 γ-corrected Burst Sizes and Weights\n",
"\n",
"No code for this section.\n",
"\n",
"## 3.6 Plotting Data\n",
"\n",
"The general form "This section of
a plotting function is:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"#dplot(d, timetrace());"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"where `d` is the
`Data` variable and `timetrace` is paper describes the general syntax for plotting in FRETBursts.\n",
"For practical reasons (i.e. we need to load the
actual data first),\n",
"these plot
function.\n", examples are reproduced later in this notebook.\n",
"\n",
"> ### See also:\n",
">\n",
"> - [bpl.timetrace](http://fretbursts.readthedocs.org/en/latest/plots.html#fretbursts.burst_plot.timetrace)\n",
"> - [bpl.ratetrace](http://fretbursts.readthedocs.org/en/latest/plots.html#fretbursts.burst_plot.ratetrace)" "To avoid errors, it is recommended \n",
"to run the notebook sequentially, without jumping section."
]
},
{
...
"- [Figures - ALEX histograms](Figures - ALEX histograms.ipynb)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Plot examples from section 3.6\n",
"\n",
"In this sections there are some examples on how to make plot with FRETBursts.\n",
"\n",
"To plot a timetrace of the measurement we use:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"dplot(d, timetrace);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Here, `dplot` is a generic wrapper (the same for all plots)\n",
"that takes care of setting up the figure, title and axis \n",
"(in the multispot case `dplot` creates multi-panel plot).\n",
"The second argument, `timetrace`, is the actual plot function. \n",
"All the eventual additional arguments passed to `dplot` are, \n",
"in turn, passed to the plot function (e.g. `timetrace`).\n",
"\n",
"If we look at the documentation for [`timetrace`](http://fretbursts.readthedocs.org/en/latest/plots.html#fretbursts.burst_plot.timetrace)\n",
"function we notice that it accepts a long list of arguments.\n",
"In python, when an argument is not specified, it will take the default\n",
"value specified in the function definition (see previus link).\n",
"\n",
"As an example, to change the bin size (i.e. duration) of the timetrace histogram,\n",
"we can look up in the [`timetrace` documentation](http://fretbursts.readthedocs.org/en/latest/plots.html#fretbursts.burst_plot.timetrace)\n",
"and find that the argument we need to modify is `binwidth`\n",
"(we can also see that the default value is `0.001` seconds).\n",
"We can then re-plot the timetrace using a bin of 0.5 ms:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"dplot(d, timetrace, binwidth=0.5e-3);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"> ### See also:\n",
">\n",
"> - [bpl.timetrace](http://fretbursts.readthedocs.org/en/latest/plots.html#fretbursts.burst_plot.timetrace)\n",
"> function documentation\n",
"> - [bpl.ratetrace](http://fretbursts.readthedocs.org/en/latest/plots.html#fretbursts.burst_plot.ratetrace)\n",
"> function documentation\n",
"> - [Plotting basics](http://nbviewer.jupyter.org/github/tritemio/FRETBursts_notebooks/blob/master/notebooks/FRETBursts%20-%20us-ALEX%20smFRET%20burst%20analysis.ipynb#Plotting-basics) in FRETBursts us-ALEX tutorial."
]
},
{
"cell_type": "markdown",
"metadata": {},
diff --git a/notebooks/Figures - ALEX histograms.ipynb b/notebooks/Figures - ALEX histograms.ipynb
index 55af5ec..5314165 100644
--- a/notebooks/Figures - ALEX histograms.ipynb
+++ b/notebooks/Figures - ALEX histograms.ipynb
...
"
\n",
"**FRETBursts: Open Source Burst Analysis Toolkit for Confocal Single-Molecule FRET**
\n",
"Ingargiola et al. (2016). biorXiv doi:[10.1101/039198](http://dx.doi.org/10.1101/039198)\n",
"
"
"\n",
"**FRETBursts: Open Source Burst Analysis Toolkit for Confocal Single-Molecule FRET**
\n",
"Ingargiola et al. (2016). biorXiv doi:[10.1101/039198](http://dx.doi.org/10.1101/039198)\n",
"
\n",
"**FRETBursts: Open Source Burst Analysis Toolkit for Confocal Single-Molecule FRET**
\n",
"Ingargiola et al. (2016). biorXiv doi:[10.1101/039198](http://dx.doi.org/10.1101/039198)\n",
"
