{ "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", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
FlyingFoxDogFacedFreeTaileLittleBroTombBatRoundEareFalseVamp
0000000
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LeafNoseHorseRhinoPangolinCatDogLlamaPigCowHippoSpermWhale
00000000300
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HumpbackWMoleHedgehogTreeShrewFlyingLemGalagoHowlerMonRhesus
000303210
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OrangutanGorillaHumanChimpanzeeJackrabbitFlyingSquOldWorldMouse
000005700
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RatNineBandeHairyArmaAnteaterSlothDugongManateeAfricanEl
00000000
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AsianElepRockHyraxTreeHyraxAardvarkGoldenMolMadagascarTenrec
0000006
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LesserEleGiantElepCaenolestPhascogaleWombatBandicoot
060000
\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", 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"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", 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" ] }, "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 }