Added python script

Author: Jb

.gitignore

@@ -121,3 +121,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# OSX stuff
+*.DS_Store

volcano_plot/volcano_plot.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python3
+
+### Script to produce volcano plots in plotly
+
+import numpy as np
+import pandas as pd
+import plotly.graph_objects as go
+
+#define significant fc and p-val thresholds
+p_thresh = 0.001
+fc_thresh = 3
+
+#helper function to assign color based on significance
+def is_significant(fc, p_val):
+    if p_val < p_thresh:
+        if fc > fc_thresh:
+            return 'red'
+        if fc < -1*fc_thresh:
+            return 'blue'
+    return 'gray'
+    
+    
+
+if __name__ == '__main__':
+
+    #import data
+    df = pd.read_csv("volcano_data.txt", sep="\t")
+
+    #assign colour based on significance
+    color = df.apply(lambda x: is_significant(x["logFC"],x['adj.P.Val']), axis= 1)
+
+    #draw plot
+    data=go.Scatter(
+        x= df['logFC'],
+        y= -1*np.log10(df['adj.P.Val']),
+        text= df['SYMBOL'],
+        hoverinfo='text',
+        mode='markers',
+        marker=dict(
+            color=color)
+    )
+
+    shapes=[
+            # Line Horizontal
+            go.layout.Shape(
+                type="line",
+                xref="paper",
+                x0=0,
+                y0=-1*np.log10(p_thresh),
+                x1=1,
+                y1=-1*np.log10(p_thresh),
+                line=dict(
+                    color="gray",
+                    width=1,
+                    dash="dash")
+            ),
+            # Line Vertical
+            go.layout.Shape(
+                type="line",
+                yref="paper",
+                x0=-1*fc_thresh,
+                y0=0,
+                x1=-1*fc_thresh,
+                y1=1,
+                line=dict(
+                    color="gray",
+                    width=1,
+                    dash="dash"
+                )
+            ),
+            # Line Vertical
+            go.layout.Shape(
+                type="line",
+                yref="paper",
+                x0=fc_thresh,
+                y0=0,
+                x1=fc_thresh,
+                y1=1,
+                line=dict(
+                    color="gray",
+                    width=1,
+                    dash="dash"
+                )
+            )]
+
+    layout= go.Layout(title="Volcano plot",
+                      xaxis = dict(title= "Log2(fold change)",
+                                range= [-1*max(abs(df['logFC'])), max(abs(df['logFC']))]),
+                      yaxis = dict(title= "-Log10(adj. p-value)"),
+                      shapes = shapes,
+                      paper_bgcolor='rgba(0,0,0,0)',
+                      plot_bgcolor='rgba(0,0,0,0)'
+                     )
+
+    fig = go.Figure(data=data, layout= layout)
+    fig.show(renderer="browser")