There are some table we would like to include in the latex document, but we first have to format them to meet the requirements. Specifically, these are the tables of significant disease enrichment results.



In [1]:

    
cd ../../HBP/









    



/home/gavin/Documents/MRes/HBP



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import csv



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import numpy as np



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from pylab import *



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ls









    



communityDetection.C@         Makefile@         README@
communityDetection.OpenMP.C@  node.h@           run@
data/                         nr3.h@            testdata/
edge.h@                       OUT/              unweightedOUT/
eigen_sym.h@                  OUTW/             unweighted_significant_disease_communities.tsv@
enrichmentStudies.h@          protounweighted/  unweighted_significant_SCH_communities.tsv@
Headers.h@                    protoweighted/    weighted_significant_disease_communities.tsv@
Helper.h@                     ran.h@            weighted_significant_SCH_communities.tsv@
ludcmp.h@                     readInputFile.h@



In [7]:

    
with open("unweighted_significant_disease_communities.tsv") as f:
    c = csv.reader(f,delimiter="\t")
    tabstrings = list(c)



In [19]:

    
t = tabstrings[1][3]



In [67]:

    
def texSI(t):
    t = "{:.2e}".format(float(t))
    t = t.split("e")
    t = r"$" + t[0] + r"\e{" + t[1] + r"}" + "$"
    return t



In [85]:

    
with open("unweighted_significant_disease_communities.tex","w") as f:
    for i,l in enumerate(tabstrings):
        if i==0:
            f.write(" ".join([r" & ".join(l[:4]+[l[-2]]), r"\\", "\n"]))
        else:
            l = l[:3] + map(texSI,l[3:6]) + l[6:]
            f.write(" ".join([r" & ".join(l[:4]+[l[-2]]), r"\\", "\n"]))



In [86]:

    
!head unweighted_significant_disease_communities.tex









    



Community & Size & disease & p-value & p_lower (%) \\ 
29 & 88 & schizophrenia & $1.69\e{-03}$ & 0.2 \\ 
2 & 99 & schizophrenia & $4.32\e{-03}$ & 0.5 \\ 
30 & 26 & Alzheimer's_disease & $5.37\e{-03}$ & 0.7 \\ 
61 & 24 & schizophrenia & $1.96\e{-02}$ & 1.5 \\ 
63 & 23 & Alzheimer's_disease & $3.50\e{-02}$ & 4.3 \\ 
61 & 24 & Alzheimer's_disease & $4.25\e{-02}$ & 4.5 \\ 
63 & 23 & schizophrenia & $4.62\e{-02}$ & 4.3 \\



In [87]:

    
with open("weighted_significant_disease_communities.tsv") as f:
    c = csv.reader(f,delimiter="\t")
    tabstrings = list(c)



In [88]:

    
with open("weighted_significant_disease_communities.tex","w") as f:
    for i,l in enumerate(tabstrings):
        if i==0:
            f.write(" ".join([r" & ".join(l[:4]+[l[-2]]), r"\\", "\n"]))
        else:
            l = l[:3] + map(texSI,l[3:6]) + l[6:]
            f.write(" ".join([r" & ".join(l[:4]+[l[-2]]), r"\\", "\n"]))