From 25b843f6bbacb1937bdb960777b73acbece64115 Mon Sep 17 00:00:00 2001
From: ziejd2
Date: Wed, 24 Feb 2021 14:36:59 -0600
Subject: GENENET8 update

---
 sourcecodes/violin_ev_plotly.py | 137 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 137 insertions(+)
 create mode 100644 sourcecodes/violin_ev_plotly.py

(limited to 'sourcecodes/violin_ev_plotly.py')

diff --git a/sourcecodes/violin_ev_plotly.py b/sourcecodes/violin_ev_plotly.py
new file mode 100644
index 00000000..69609d94
--- /dev/null
+++ b/sourcecodes/violin_ev_plotly.py
@@ -0,0 +1,137 @@
+#!/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_evidence.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")
+#varNames = line
+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])
+
+#Get the variables with evidence
+evfile=netID+"varname.txt"
+evf=open(evfile,"r")
+line=evf.readline()
+#ev_vars = map(string.strip,line.strip().split("\t"))
+ev_vars = line.strip().split("\t")
+keepVars = []
+for i in cNames:
+    if i not in ev_vars:
+        keepVars.append(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_evidence.txt"
+f2=open(filename2,"r")
+line = f2.readline()
+pdf_varName = []
+pdf_data = []
+while line:
+    line = line.strip()
+    if line == "Data for new node":
+        line = f2.readline()
+        pdf_varName.append(line.strip())
+        line = f2.readline()
+        pdf_data.append([line.strip()])
+    else:
+        pdf_data[-1].append(float(line.strip()))
+    line = f2.readline()
+
+layout = go.Layout(
+    title="Distributions considering evidence",
+    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)
+
+icount = 0
+for i in range(len(keepVars)):
+    for j in range(len(cNames)):
+        if keepVars[i] == cNames[j]:
+            idata = j
+            break
+    for j in range(len(pdf_varName)):
+        if keepVars[i] == pdf_varName[j]:
+            ipdf = j
+            break
+    y = []
+    for j in range(len(data)):
+        y.append(data[j][idata])
+    y_stand = standardize(y)
+    #Add traces to violin plot
+    if icount == 0:
+        fig.add_trace(go.Violin(y=y_stand,x0=cNames[idata],side='negative',legendgroup='Data',name='Fit to original data',fillcolor='blue',line=dict(color='blue'),hoverinfo='none',points='all',scalegroup=cNames[idata]))
+        fig.add_trace(go.Violin(y=pdf_data[ipdf],x0=cNames[idata],side='positive',legendgroup='Network parameters considering evidence',name='Network parameters considering evidence',fillcolor='orange',line=dict(color='orange'),hoverinfo='none',points=False,scalegroup=cNames[idata]))
+        icount = 1
+    else:
+        fig.add_trace(go.Violin(y=y_stand,x0=cNames[idata],side='negative',legendgroup='Data',name='Data',fillcolor='blue',line=dict(color='blue'),showlegend=False,hoverinfo='none',points='all',scalegroup=cNames[idata]))
+        fig.add_trace(go.Violin(y=pdf_data[ipdf],x0=cNames[idata],side='positive',legendgroup='Network parameters considering evidence',name='Network parameters considering evidence',fillcolor='orange',line=dict(color='orange'),showlegend=False,hoverinfo='none',points=False,scalegroup=cNames[idata]))
+
+
+plotly.offline.plot(fig,filename=outfile)
+
-- 
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