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All `cogent3` sequence collections classes (`SequenceCollection`, `Alignment` and `ArrayAlignment`) have a dotplot method.\n", "\n", "The method returns a drawable, as demonstrated below between unaligned sequences." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "pycharm": { "is_executing": false } }, "outputs": [ { "data": { "text/html": [ " \n", " " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.plotly.v1+json": { "config": { "plotlyServerURL": "https://plot.ly" }, "data": [ { "line": { "color": "blue" }, "mode": "lines", "name": "+ strand", "type": "scatter", "x": [ 2253, 2277, null, 2055, 2076, null, 2102, 2123, null, 1938, 1960, null, 1927, 1948, null, 1929, 1950, null, 1760, 1781, null, 1916, 1937, null, 1862, 1883, null, 1651, 1673, null, 1658, 1681, null, 2118, 2139, null, 1634, 1655, null, 1633, 1654, null, 2214, 2236, null, 1641, 1663, null, 2053, 2076, null, 1634, 1658, null, 1560, 1581, null, 1511, 1535, null, 1934, 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\n", " \n", " \n", "
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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from cogent3 import load_unaligned_seqs\n", "\n", "seqs = load_unaligned_seqs(\"../data/SCA1-cds.fasta\", moltype=\"dna\")\n", "draw = seqs.dotplot()\n", "draw.show()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If sequence names are not provided, two randomly chosen sequences are selected (see below). The plot title reflects the parameter values for defining a match. `window` is the size of the sequence segments being compared. `threshold` is the number of exact matches within `window` required for the two sequence segments to be considered a match. `gap` is the size of a gap between adjacent matches before merging." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Modifying the matching parameters\n", "\n", "If we set window and threshold to be equal, this is equivalent to an exact match approach." ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "pycharm": { "is_executing": false } }, "outputs": [ { "data": { "text/html": [ " \n", " " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.plotly.v1+json": { "config": { "plotlyServerURL": "https://plot.ly" }, "data": [ { "line": { "color": "blue" }, "mode": "lines", "name": "+ strand", "type": "scatter", "x": [ 2141, 2150, null, 2363, 2372, null, 1811, 1820, null, 1961, 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"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": "Window=20, Matched ≥ 14/20 & Gap ≤ 0" }, "width": 500, "xaxis": { "mirror": true, "range": [ 0, 2445 ], "showgrid": false, "showline": true, "title": { "text": "Human" }, "visible": true }, "yaxis": { "mirror": true, "range": [ 0, 2397 ], "showgrid": false, "showline": true, "title": { "text": "Mouse" }, "visible": true } } }, "text/html": [ "
\n", " \n", " \n", "
\n", " \n", "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "draw = seqs.dotplot(name1=\"Human\", name2=\"Mouse\", rc=True)\n", "draw.show()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**NOTE:** clicking on an entry in the legend turns it off" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setting plot attributes\n", "\n", "I'll modify the title and figure width. 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "draw = seqs.dotplot(name1=\"Human\", name2=\"Mouse\", rc=True, title=\"SCA1\", width=400)\n", "draw.show()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## All options" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "pycharm": { "is_executing": false } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Help on method dotplot in module cogent3.core.alignment:\n", "\n", "dotplot(name1=None, name2=None, window=20, threshold=None, min_gap=0, width=500, title=None, rc=False, show_progress=False) method of cogent3.core.alignment.SequenceCollection instance\n", " make a dotplot between specified sequences. Random sequences\n", " chosen if names not provided.\n", " \n", " Parameters\n", " ----------\n", " name1, name2 : str or None\n", " names of sequences. If one is not provided, a random choice is made\n", " window : int\n", " k-mer size for comparison between sequences\n", " threshold : int\n", " windows where the sequences are identical >= threshold are a match\n", " min_gap : int\n", " permitted gap for joining adjacent line segments, default is no gap\n", " joining\n", " width : int\n", " figure width. Figure height is computed based on the ratio of\n", " len(seq1) / len(seq2)\n", " title\n", " title for the plot\n", " rc : bool or None\n", " include dotplot of reverse compliment also. Only applies to Nucleic\n", " acids moltypes\n", " Returns\n", " -------\n", " a Drawable or AnnotatedDrawable\n", "\n" ] } ], "source": [ "help(seqs.dotplot)" ] } ], "metadata": { "kernelspec": { "display_name": "Python [conda env:c3dev] *", "language": "python", "name": "conda-env-c3dev-py" }, "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 }