manhattan plot is ready to go

Author: holtzy

src/notebooks/manhattan-plot-with-matplotlib.ipynb

@@ -4,14 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Manhattan Plot with Matplotlib"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "**Manhattan plot** is a type of scatterplot which is mostly used in genome-wide association studies (GWAS). Each point represents a genetic variant. X axis value represents its position on the chromosome and the value on the y-axis represents the −log10 of the P value.\n",
+    "A [Manhattan plot](https://en.wikipedia.org/wiki/Manhattan_plot#:~:text=A%20Manhattan%20plot%20is%20a,GWAS)%20to%20display%20significant%20SNPs.) is a variation of a [scatterplot](https://www.python-graph-gallery.com/scatter-plot/). It is used in genome-wide association studies (GWAS). Each point represents a genetic variant. Its X axis value represents its position on the chromosome and the value on the y-axis represents the `−log10` of its P value.\n",
     "\n",
     "[Elad Joseph](https://stackoverflow.com/users/2807860/elad-joseph) suggested this nice solution on [stackoverflow](https://stackoverflow.com/questions/37463184/how-to-create-a-manhattan-plot-with-matplotlib-in-python) to build a manhattan plot with matplotlib and pandas:"
    ]
@@ -80,18 +73,32 @@
     "# show the graph\n",
     "plt.show()"
    ]
+  },
+  {
+   "source": [
+    "Et voila! A nice Manhattan plot allowing to check for phenotype - genotype associations!"
+   ],
+   "cell_type": "markdown",
+   "metadata": {}
+  },
+  {
+   "source": [
+    "> Note: if you're willing to build a manhattan plot with R, [this blogpost](https://www.r-graph-gallery.com/101_Manhattan_plot.html) should interest you"
+   ],
+   "cell_type": "markdown",
+   "metadata": {}
   }
  ],
  "metadata": {
   "chartType": "scatter",
-  "description": "This post explains how to build a <b>manhattan plot</b> in python and provides a reproducible code.",
+  "description": "This post explains how to build a <b>manhattan plot</b> using <code>python</code> and <code>matplotlib</code>. A manhattan plot is commonly used by geneticians for genome-wide association study.",
   "family": "correlation",
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
-  "keywords": "python, chart, plot, seaborn, matplotlib, scatterplot, manhattan",
+  "keywords": "python, chart, plot, seaborn, matplotlib, scatterplot, manhattan, genetics, gwas",
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
@@ -104,10 +111,10 @@
    "pygments_lexer": "ipython3",
    "version": "3.7.3"
   },
-  "seoDescription": "How to draw a manhattan plot with matplotlib",
+  "seoDescription": "How to draw a manhattan plot with python and matplotlib for genetics analysis",
   "slug": "manhattan-plot-with-matplotlib",
-  "title": "Manhattan Plot with Matplotlib"
+  "title": "Manhattan Plot with Python and Matplotlib"
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

src/pages/scatter-plot.js

@@ -197,6 +197,11 @@ export default function ViolinPlot() {
             caption="Add an annotation to highlight a specific marker"
             linkTo="/193-annotate-matplotlib-chart"
           />
+          <ChartImageContainer
+            imgName="manhattan-plot-with-matplotlib"
+            caption="How to build a Manhattan plot with Python and Matplotlib"
+            linkTo="/manhattan-plot-with-matplotlib"
+          />
         </Row>
       </Container>