{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Counting gaps per sequence\n",
"\n",
"We have several different ways of counting sequence gaps, and of visualising the results. By default, the `count_gaps_per_seq()` method returns a matrix of counts without the ability to visualise the results. When setting the argument `unique=True`, the counts are for gaps uniquely induced by each sequence. This can be a useful indicator of highly divergent sequences."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"
\n",
"\n",
"\n",
"FlyingFox | \n",
"DogFaced | \n",
"FreeTaile | \n",
"LittleBro | \n",
"TombBat | \n",
"RoundEare | \n",
"FalseVamp | \n",
"\n",
"\n",
"\n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"LeafNose | \n",
"Horse | \n",
"Rhino | \n",
"Pangolin | \n",
"Cat | \n",
"Dog | \n",
"Llama | \n",
"Pig | \n",
"Cow | \n",
"Hippo | \n",
"SpermWhale | \n",
"\n",
"\n",
"\n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"3 | \n",
"0 | \n",
"0 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"HumpbackW | \n",
"Mole | \n",
"Hedgehog | \n",
"TreeShrew | \n",
"FlyingLem | \n",
"Galago | \n",
"HowlerMon | \n",
"Rhesus | \n",
"\n",
"\n",
"\n",
"0 | \n",
"0 | \n",
"0 | \n",
"3 | \n",
"0 | \n",
"3 | \n",
"21 | \n",
"0 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"Orangutan | \n",
"Gorilla | \n",
"Human | \n",
"Chimpanzee | \n",
"Jackrabbit | \n",
"FlyingSqu | \n",
"OldWorld | \n",
"Mouse | \n",
"\n",
"\n",
"\n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"57 | \n",
"0 | \n",
"0 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"Rat | \n",
"NineBande | \n",
"HairyArma | \n",
"Anteater | \n",
"Sloth | \n",
"Dugong | \n",
"Manatee | \n",
"AfricanEl | \n",
"\n",
"\n",
"\n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"AsianElep | \n",
"RockHyrax | \n",
"TreeHyrax | \n",
"Aardvark | \n",
"GoldenMol | \n",
"Madagascar | \n",
"Tenrec | \n",
"\n",
"\n",
"\n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"6 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"LesserEle | \n",
"GiantElep | \n",
"Caenolest | \n",
"Phascogale | \n",
"Wombat | \n",
"Bandicoot | \n",
"\n",
"\n",
"\n",
"0 | \n",
"6 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"0 | \n",
"
\n",
"\n",
"
\n"
],
"text/plain": [
"=================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================\n",
"FlyingFox DogFaced FreeTaile LittleBro TombBat RoundEare FalseVamp LeafNose Horse Rhino Pangolin Cat Dog Llama Pig Cow Hippo SpermWhale HumpbackW Mole Hedgehog TreeShrew FlyingLem Galago HowlerMon Rhesus Orangutan Gorilla Human Chimpanzee Jackrabbit FlyingSqu OldWorld Mouse Rat NineBande HairyArma Anteater Sloth Dugong Manatee AfricanEl AsianElep RockHyrax TreeHyrax Aardvark GoldenMol Madagascar Tenrec LesserEle GiantElep Caenolest Phascogale Wombat Bandicoot\n",
"-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 3 0 3 21 0 0 0 0 0 0 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 6 0 0 0 0\n",
"-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from cogent3 import load_aligned_seqs\n",
"\n",
"aln = load_aligned_seqs('../../tests/data/brca1.fasta', moltype='dna')\n",
"\n",
"counts = aln.count_gaps_per_seq(unique=True)\n",
"counts"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Plotting counts of unique gaps\n",
"\n",
"There are three plot types supported. In all cases, placing the mouse pointer over a data point will show hover text with the sequence name."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Displaying unique gaps as a bar chart"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
" \n",
" "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"type": "bar",
"x": [
"FlyingFox",
"DogFaced",
"FreeTaile",
"LittleBro",
"TombBat",
"RoundEare",
"FalseVamp",
"LeafNose",
"Horse",
"Rhino",
"Pangolin",
"Cat",
"Dog",
"Llama",
"Pig",
"Cow",
"Hippo",
"SpermWhale",
"HumpbackW",
"Mole",
"Hedgehog",
"TreeShrew",
"FlyingLem",
"Galago",
"HowlerMon",
"Rhesus",
"Orangutan",
"Gorilla",
"Human",
"Chimpanzee",
"Jackrabbit",
"FlyingSqu",
"OldWorld",
"Mouse",
"Rat",
"NineBande",
"HairyArma",
"Anteater",
"Sloth",
"Dugong",
"Manatee",
"AfricanEl",
"AsianElep",
"RockHyrax",
"TreeHyrax",
"Aardvark",
"GoldenMol",
"Madagascar",
"Tenrec",
"LesserEle",
"GiantElep",
"Caenolest",
"Phascogale",
"Wombat",
"Bandicoot"
],
"y": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
3,
0,
0,
0,
0,
0,
3,
0,
3,
21,
0,
0,
0,
0,
0,
0,
57,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
6,
0,
6,
0,
0,
0,
0
]
}
],
"layout": {
"autosize": false,
"font": {
"family": "Balto",
"size": 14
},
"hovermode": "closest",
"margin": {
"b": 50,
"l": 50,
"pad": 4,
"r": 50,
"t": 50
},
"showlegend": false,
"template": {
"data": {
"bar": [
{
"error_x": {
"color": "#2a3f5f"
},
"error_y": {
"color": "#2a3f5f"
},
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
}
},
"type": "bar"
}
],
"barpolar": [
{
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
}
},
"type": "barpolar"
}
],
"carpet": [
{
"aaxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"baxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"type": "carpet"
}
],
"choropleth": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "choropleth"
}
],
"contour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "contour"
}
],
"contourcarpet": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "contourcarpet"
}
],
"heatmap": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "heatmap"
}
],
"heatmapgl": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "heatmapgl"
}
],
"histogram": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "histogram"
}
],
"histogram2d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "histogram2d"
}
],
"histogram2dcontour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "histogram2dcontour"
}
],
"mesh3d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "mesh3d"
}
],
"parcoords": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "parcoords"
}
],
"pie": [
{
"automargin": true,
"type": "pie"
}
],
"scatter": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter"
}
],
"scatter3d": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter3d"
}
],
"scattercarpet": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattercarpet"
}
],
"scattergeo": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergeo"
}
],
"scattergl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergl"
}
],
"scattermapbox": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermapbox"
}
],
"scatterpolar": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolar"
}
],
"scatterpolargl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolargl"
}
],
"scatterternary": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterternary"
}
],
"surface": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "surface"
}
],
"table": [
{
"cells": {
"fill": {
"color": "#EBF0F8"
},
"line": {
"color": "white"
}
},
"header": {
"fill": {
"color": "#C8D4E3"
},
"line": {
"color": "white"
}
},
"type": "table"
}
]
},
"layout": {
"annotationdefaults": {
"arrowcolor": "#2a3f5f",
"arrowhead": 0,
"arrowwidth": 1
},
"coloraxis": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"colorscale": {
"diverging": [
[
0,
"#8e0152"
],
[
0.1,
"#c51b7d"
],
[
0.2,
"#de77ae"
],
[
0.3,
"#f1b6da"
],
[
0.4,
"#fde0ef"
],
[
0.5,
"#f7f7f7"
],
[
0.6,
"#e6f5d0"
],
[
0.7,
"#b8e186"
],
[
0.8,
"#7fbc41"
],
[
0.9,
"#4d9221"
],
[
1,
"#276419"
]
],
"sequential": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"sequentialminus": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
]
},
"colorway": [
"#636efa",
"#EF553B",
"#00cc96",
"#ab63fa",
"#FFA15A",
"#19d3f3",
"#FF6692",
"#B6E880",
"#FF97FF",
"#FECB52"
],
"font": {
"color": "#2a3f5f"
},
"geo": {
"bgcolor": "white",
"lakecolor": "white",
"landcolor": "#E5ECF6",
"showlakes": true,
"showland": true,
"subunitcolor": "white"
},
"hoverlabel": {
"align": "left"
},
"hovermode": "closest",
"mapbox": {
"style": "light"
},
"paper_bgcolor": "white",
"plot_bgcolor": "#E5ECF6",
"polar": {
"angularaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"radialaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"scene": {
"xaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"yaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"zaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
}
},
"shapedefaults": {
"line": {
"color": "#2a3f5f"
}
},
"ternary": {
"aaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"baxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"caxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"title": {
"x": 0.05
},
"xaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
},
"yaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
}
}
},
"title": {
"text": "Gaps Per Sequence"
},
"width": 500,
"xaxis": {
"visible": true
},
"yaxis": {
"title": {
"text": "Gap counts"
},
"visible": true
}
}
},
"text/html": [
"\n",
" \n",
" \n",
"
\n",
" \n",
"
"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"counts = aln.count_gaps_per_seq(unique=True, drawable='bar')\n",
"counts.show(width=500)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Displaying unique gaps as a violin plot"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
" \n",
" "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"name": "brca1.fasta",
"text": [
"FlyingFox",
"DogFaced",
"FreeTaile",
"LittleBro",
"TombBat",
"RoundEare",
"FalseVamp",
"LeafNose",
"Horse",
"Rhino",
"Pangolin",
"Cat",
"Dog",
"Llama",
"Pig",
"Cow",
"Hippo",
"SpermWhale",
"HumpbackW",
"Mole",
"Hedgehog",
"TreeShrew",
"FlyingLem",
"Galago",
"HowlerMon",
"Rhesus",
"Orangutan",
"Gorilla",
"Human",
"Chimpanzee",
"Jackrabbit",
"FlyingSqu",
"OldWorld",
"Mouse",
"Rat",
"NineBande",
"HairyArma",
"Anteater",
"Sloth",
"Dugong",
"Manatee",
"AfricanEl",
"AsianElep",
"RockHyrax",
"TreeHyrax",
"Aardvark",
"GoldenMol",
"Madagascar",
"Tenrec",
"LesserEle",
"GiantElep",
"Caenolest",
"Phascogale",
"Wombat",
"Bandicoot"
],
"type": "violin",
"y": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
3,
0,
0,
0,
0,
0,
3,
0,
3,
21,
0,
0,
0,
0,
0,
0,
57,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
6,
0,
6,
0,
0,
0,
0
]
}
],
"layout": {
"autosize": false,
"font": {
"family": "Balto",
"size": 14
},
"height": 500,
"hovermode": "closest",
"margin": {
"b": 50,
"l": 50,
"pad": 4,
"r": 50,
"t": 50
},
"showlegend": false,
"template": {
"data": {
"bar": [
{
"error_x": {
"color": "#2a3f5f"
},
"error_y": {
"color": "#2a3f5f"
},
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
}
},
"type": "bar"
}
],
"barpolar": [
{
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
}
},
"type": "barpolar"
}
],
"carpet": [
{
"aaxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"baxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"type": "carpet"
}
],
"choropleth": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "choropleth"
}
],
"contour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "contour"
}
],
"contourcarpet": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "contourcarpet"
}
],
"heatmap": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "heatmap"
}
],
"heatmapgl": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "heatmapgl"
}
],
"histogram": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "histogram"
}
],
"histogram2d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "histogram2d"
}
],
"histogram2dcontour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "histogram2dcontour"
}
],
"mesh3d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "mesh3d"
}
],
"parcoords": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "parcoords"
}
],
"pie": [
{
"automargin": true,
"type": "pie"
}
],
"scatter": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter"
}
],
"scatter3d": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter3d"
}
],
"scattercarpet": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattercarpet"
}
],
"scattergeo": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergeo"
}
],
"scattergl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergl"
}
],
"scattermapbox": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermapbox"
}
],
"scatterpolar": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolar"
}
],
"scatterpolargl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolargl"
}
],
"scatterternary": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterternary"
}
],
"surface": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "surface"
}
],
"table": [
{
"cells": {
"fill": {
"color": "#EBF0F8"
},
"line": {
"color": "white"
}
},
"header": {
"fill": {
"color": "#C8D4E3"
},
"line": {
"color": "white"
}
},
"type": "table"
}
]
},
"layout": {
"annotationdefaults": {
"arrowcolor": "#2a3f5f",
"arrowhead": 0,
"arrowwidth": 1
},
"coloraxis": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"colorscale": {
"diverging": [
[
0,
"#8e0152"
],
[
0.1,
"#c51b7d"
],
[
0.2,
"#de77ae"
],
[
0.3,
"#f1b6da"
],
[
0.4,
"#fde0ef"
],
[
0.5,
"#f7f7f7"
],
[
0.6,
"#e6f5d0"
],
[
0.7,
"#b8e186"
],
[
0.8,
"#7fbc41"
],
[
0.9,
"#4d9221"
],
[
1,
"#276419"
]
],
"sequential": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"sequentialminus": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
]
},
"colorway": [
"#636efa",
"#EF553B",
"#00cc96",
"#ab63fa",
"#FFA15A",
"#19d3f3",
"#FF6692",
"#B6E880",
"#FF97FF",
"#FECB52"
],
"font": {
"color": "#2a3f5f"
},
"geo": {
"bgcolor": "white",
"lakecolor": "white",
"landcolor": "#E5ECF6",
"showlakes": true,
"showland": true,
"subunitcolor": "white"
},
"hoverlabel": {
"align": "left"
},
"hovermode": "closest",
"mapbox": {
"style": "light"
},
"paper_bgcolor": "white",
"plot_bgcolor": "#E5ECF6",
"polar": {
"angularaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"radialaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"scene": {
"xaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"yaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"zaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
}
},
"shapedefaults": {
"line": {
"color": "#2a3f5f"
}
},
"ternary": {
"aaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"baxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"caxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"title": {
"x": 0.05
},
"xaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
},
"yaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
}
}
},
"title": {
"text": "Gaps Per Sequence"
},
"width": 300,
"xaxis": {
"visible": true
},
"yaxis": {
"title": {
"text": "Gap counts"
},
"visible": true
}
}
},
"text/html": [
"\n",
" \n",
" \n",
"
\n",
" \n",
"
"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"counts = aln.count_gaps_per_seq(unique=True, drawable='violin')\n",
"counts.show(width=300, height=500)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Displaying unique gaps as a box plot"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
" \n",
" "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"name": "brca1.fasta",
"text": [
"FlyingFox",
"DogFaced",
"FreeTaile",
"LittleBro",
"TombBat",
"RoundEare",
"FalseVamp",
"LeafNose",
"Horse",
"Rhino",
"Pangolin",
"Cat",
"Dog",
"Llama",
"Pig",
"Cow",
"Hippo",
"SpermWhale",
"HumpbackW",
"Mole",
"Hedgehog",
"TreeShrew",
"FlyingLem",
"Galago",
"HowlerMon",
"Rhesus",
"Orangutan",
"Gorilla",
"Human",
"Chimpanzee",
"Jackrabbit",
"FlyingSqu",
"OldWorld",
"Mouse",
"Rat",
"NineBande",
"HairyArma",
"Anteater",
"Sloth",
"Dugong",
"Manatee",
"AfricanEl",
"AsianElep",
"RockHyrax",
"TreeHyrax",
"Aardvark",
"GoldenMol",
"Madagascar",
"Tenrec",
"LesserEle",
"GiantElep",
"Caenolest",
"Phascogale",
"Wombat",
"Bandicoot"
],
"type": "box",
"y": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
3,
0,
0,
0,
0,
0,
3,
0,
3,
21,
0,
0,
0,
0,
0,
0,
57,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
6,
0,
6,
0,
0,
0,
0
]
}
],
"layout": {
"autosize": false,
"font": {
"family": "Balto",
"size": 14
},
"height": 500,
"hovermode": "closest",
"margin": {
"b": 50,
"l": 50,
"pad": 4,
"r": 50,
"t": 50
},
"showlegend": false,
"template": {
"data": {
"bar": [
{
"error_x": {
"color": "#2a3f5f"
},
"error_y": {
"color": "#2a3f5f"
},
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
}
},
"type": "bar"
}
],
"barpolar": [
{
"marker": {
"line": {
"color": "#E5ECF6",
"width": 0.5
}
},
"type": "barpolar"
}
],
"carpet": [
{
"aaxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"baxis": {
"endlinecolor": "#2a3f5f",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "#2a3f5f"
},
"type": "carpet"
}
],
"choropleth": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "choropleth"
}
],
"contour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "contour"
}
],
"contourcarpet": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "contourcarpet"
}
],
"heatmap": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "heatmap"
}
],
"heatmapgl": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "heatmapgl"
}
],
"histogram": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "histogram"
}
],
"histogram2d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "histogram2d"
}
],
"histogram2dcontour": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "histogram2dcontour"
}
],
"mesh3d": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"type": "mesh3d"
}
],
"parcoords": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "parcoords"
}
],
"pie": [
{
"automargin": true,
"type": "pie"
}
],
"scatter": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter"
}
],
"scatter3d": [
{
"line": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatter3d"
}
],
"scattercarpet": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattercarpet"
}
],
"scattergeo": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergeo"
}
],
"scattergl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattergl"
}
],
"scattermapbox": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scattermapbox"
}
],
"scatterpolar": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolar"
}
],
"scatterpolargl": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterpolargl"
}
],
"scatterternary": [
{
"marker": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"type": "scatterternary"
}
],
"surface": [
{
"colorbar": {
"outlinewidth": 0,
"ticks": ""
},
"colorscale": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"type": "surface"
}
],
"table": [
{
"cells": {
"fill": {
"color": "#EBF0F8"
},
"line": {
"color": "white"
}
},
"header": {
"fill": {
"color": "#C8D4E3"
},
"line": {
"color": "white"
}
},
"type": "table"
}
]
},
"layout": {
"annotationdefaults": {
"arrowcolor": "#2a3f5f",
"arrowhead": 0,
"arrowwidth": 1
},
"coloraxis": {
"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"colorscale": {
"diverging": [
[
0,
"#8e0152"
],
[
0.1,
"#c51b7d"
],
[
0.2,
"#de77ae"
],
[
0.3,
"#f1b6da"
],
[
0.4,
"#fde0ef"
],
[
0.5,
"#f7f7f7"
],
[
0.6,
"#e6f5d0"
],
[
0.7,
"#b8e186"
],
[
0.8,
"#7fbc41"
],
[
0.9,
"#4d9221"
],
[
1,
"#276419"
]
],
"sequential": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
],
"sequentialminus": [
[
0.0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1.0,
"#f0f921"
]
]
},
"colorway": [
"#636efa",
"#EF553B",
"#00cc96",
"#ab63fa",
"#FFA15A",
"#19d3f3",
"#FF6692",
"#B6E880",
"#FF97FF",
"#FECB52"
],
"font": {
"color": "#2a3f5f"
},
"geo": {
"bgcolor": "white",
"lakecolor": "white",
"landcolor": "#E5ECF6",
"showlakes": true,
"showland": true,
"subunitcolor": "white"
},
"hoverlabel": {
"align": "left"
},
"hovermode": "closest",
"mapbox": {
"style": "light"
},
"paper_bgcolor": "white",
"plot_bgcolor": "#E5ECF6",
"polar": {
"angularaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"radialaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"scene": {
"xaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"yaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"zaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
}
},
"shapedefaults": {
"line": {
"color": "#2a3f5f"
}
},
"ternary": {
"aaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"baxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"caxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"title": {
"x": 0.05
},
"xaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
},
"yaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
}
}
},
"title": {
"text": "Gaps Per Sequence"
},
"width": 300,
"xaxis": {
"visible": true
},
"yaxis": {
"title": {
"text": "Gap counts"
},
"visible": true
}
}
},
"text/html": [
"\n",
" \n",
" \n",
"
\n",
" \n",
"
"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"counts = aln.count_gaps_per_seq(unique=True, drawable='box')\n",
"counts.show(width=300, height=500)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.1"
},
"pycharm": {
"stem_cell": {
"cell_type": "raw",
"metadata": {
"collapsed": false
},
"source": []
}
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
}
},
"nbformat": 4,
"nbformat_minor": 4
}