GENENET8 update

1 files changed, 123 insertions, 0 deletions

diff --git a/sourcecodes/violin_plotly.py b/sourcecodes/violin_plotly.py
new file mode 100644
index 00000000..8e0f8ea2
--- /dev/null
+++ b/sourcecodes/violin_plotly.py
@@ -0,0 +1,123 @@
+#!/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3
+import os
+import sys
+import math
+#sys.path.append('/home/jziebart/.local/bin')
+#sys.path.append('/home/jziebart/.local/lib')
+
+
+import plotly
+import plotly.graph_objs as go
+import csv
+import string
+
+def mean_stdev(y):
+    mean = sum(y)
+    mean = sum(y)/len(y)
+    stdev = 0
+    for yi in y:
+        stdev = stdev + (yi - mean)**2
+    stdev = stdev/(len(y)-1)
+    stdev = math.sqrt(stdev)
+    return mean,stdev;
+
+def standardize(y):
+    mean,stdev = mean_stdev(y)
+    ystd = []
+    for yi in y:
+        yi = (yi - mean)/stdev
+        ystd.append(yi)
+    return ystd
+
+
+netID = sys.argv[-1]
+outfile = netID+"violin_plotly.html"
+
+ 
+filename=netID+"continuous_input.txt"
+f=open(filename,"r")
+#Read the first line to get the variable names
+line=f.readline()
+#line = map(string.strip,line.strip().split("\t"))
+varNames = line.strip().split("\t")
+line=f.readline()
+#line = map(string.strip,line.strip().split("\t"))
+line = line.strip().split("\t")
+for i in range(len(line)):
+    line[i] = int(line[i])
+cd_types = line
+cNames = []
+for i in range(len(varNames)):
+    if cd_types[i] == 1:
+        cNames.append(varNames[i])
+
+#Read in original data
+data = []
+line = f.readline()
+while line:
+    #line = map(string.strip,line.strip().split("\t"))
+    line = line.strip().split("\t")
+    temp = []
+    for i in range(len(varNames)):
+        if cd_types[i] == 1:
+            temp.append(float(line[i]))
+    data.append(temp)
+    line = f.readline()
+
+#Read in data for violin plots
+filename2=netID+"violin_orig.txt"
+f2=open(filename2,"r")
+line = f2.readline()
+pdf_data = []
+while line:
+    line = line.strip()
+    if line == "Data for new node":
+        line = f2.readline()
+        pdf_data.append([line.strip()])
+    else:
+        pdf_data[-1].append(float(line.strip()))
+    line = f2.readline()
+
+pdf_data2 = []
+for i in range(len(cNames)):
+    for j in range(len(pdf_data)):
+        if cNames[i] == pdf_data[j][0]:
+            pdf_data2.append(pdf_data[j][1:])
+
+del pdf_data
+
+layout = go.Layout(
+    title="Original distributions",
+    titlefont=dict(
+        family='Arial, sans-serif',
+        size=24,
+        color='black'
+        ),
+    title_xref="paper",
+    title_x=0.5,
+    title_xanchor="center",
+    title_yanchor="middle",
+    yaxis=dict(title="Distributions of standardized data"),
+    legend=dict(orientation='h'),
+    margin=dict(t=40,l=70,b=40)
+)
+fig = go.Figure(layout=layout)
+
+for i in range(len(cNames)):
+    y = []
+    for j in range(len(data)):
+        y.append(data[j][i])
+    y_stand = standardize(y)
+    #Add traces to violin plot
+    if i == 1:
+        fig.add_trace(go.Violin(y=y_stand,x0=cNames[i],side='negative',legendgroup='Data',name='Fit to data',fillcolor='blue',line=dict(color='blue'),hoverinfo='none',points='all',scalegroup=cNames[i]))
+        fig.add_trace(go.Violin(y=pdf_data2[i],x0=cNames[i],side='positive',legendgroup='Network parameters',name='Network parameters',fillcolor='orange',line=dict(color='orange'),hoverinfo='none',points=False,scalegroup=cNames[i]))
+    else:
+        fig.add_trace(go.Violin(y=y_stand,x0=cNames[i],side='negative',legendgroup='Data',name='Data',fillcolor='blue',line=dict(color='blue'),showlegend=False,hoverinfo='none',points='all',scalegroup=cNames[i]))
+        fig.add_trace(go.Violin(y=pdf_data2[i],x0=cNames[i],side='positive',legendgroup='Network parameters',name='Network parameters',fillcolor='orange',line=dict(color='orange'),showlegend=False,hoverinfo='none',points=False,scalegroup=cNames[i]))
+
+
+fig.update_layout(title_xanchor="center")
+
+plotly.offline.plot(fig,filename=outfile)
+