Plots tables from aDiff/cuffdiff into cytoscape using String protein queries. 
    Uses top changed genes as well as first neighbours and difusion fo generate subnetworks. 
    
    :param df: df as outputed by aDiff for differential gene expression
    :param aging_genes: ENS gene ids to be labeled with a diagonal
    :param species: species for string app query. eg. "caenorhabditis elegans", "drosophila melanogaster", "mus musculus", "homo sapiens"
    :param limit: limit for string app query. Number of extra genes to recover. If None, limit=N(query_genes)*.25
    :param cuttoff: confidence cuttoff for sting app query. Default=0.4
    :param taxon: taxon id for string app query. For the species shown above, taxon id will be automatically identified
    :param cytoscape_host: host address for cytoscape
    :param cytoscape_port: cytoscape port
    :param target: target destination for saving files without prefix. eg. "/beegfs/group_bit/home/JBoucas/test/N2_vs_daf2"

    :returns: nothing

def aDiffCytoscape(df,aging_genes,target,species="caenorhabditis elegans",limit=None, cutoff=0.4,\
                  taxon=None,host=cytoscape_host,port=cytoscape_port):
    """
    Plots tables from aDiff/cuffdiff into cytoscape using String protein queries. 
    Uses top changed genes as well as first neighbours and difusion fo generate subnetworks. 
    
    :param df: df as outputed by aDiff for differential gene expression
    :param aging_genes: ENS gene ids to be labeled with a diagonal
    :param species: species for string app query. eg. "caenorhabditis elegans", "drosophila melanogaster", "mus musculus", "homo sapiens"
    :param limit: limit for string app query. Number of extra genes to recover. If None, limit=N(query_genes)*.25
    :param cuttoff: confidence cuttoff for sting app query. Default=0.4
    :param taxon: taxon id for string app query. For the species shown above, taxon id will be automatically identified
    :param cytoscape_host: host address for cytoscape
    :param cytoscape_port: cytoscape port
    :param target: target destination for saving files without prefix. eg. "/beegfs/group_bit/home/JBoucas/test/N2_vs_daf2"

    :returns: nothing
    
    """

    ##### TEMPORARY FIX - STRING APP NOT ACCEPTING QUERIES ABOVE 2000 GENES ####
    df=df.sort_values(by=["q_value"],ascending=True)
    df.reset_index(inplace=True, drop=True)
    tmp=df[:1999]
    df=tmp.copy()
    ##### END OF TEMPORARY FIX #####

    query_genes=df["ensembl_gene_id"].tolist()
    df["NormInt"]=df["value_1"]*df["value_2"]
    df["NormInt"]=df["NormInt"].apply(lambda x: np.log10(np.sqrt(x)) )

    if not limit:
        limit=int(len(query_genes)*.25)

    # Annotate aging evindence
    def CheckEvidence(x,aging_genes=aging_genes):
        if x in aging_genes:
            res="aging_gene"
        else:
            res="no"
        return res
    df["evidence"]=df["ensembl_gene_id"].apply(lambda x:CheckEvidence(x) )

    # fix infinit values
    def FixInfs(x):
        if str(x) in ["-inf","inf"]:
            res=np.nan
        else:
            res=x
            return res
    df["NormInt"]=df["NormInt"].apply( lambda x:  FixInfs(x) )
    df["log2(fold_change)"]=df["log2(fold_change)"].apply( lambda x:  FixInfs(x) )
        
    taxons={"caenorhabditis elegans":"6239","drosophila melanogaster":"7227",\
       "mus musculus":"10090","homo sapiens":"9606"}
    if not taxon: 
        taxon=taxons[species]


    # destroy any existing network still present in cytoscape
    response=cytoscape("network", "list",\
                       host=host, port=port)
    if "networks" in response.keys():
        response=response["networks"]
        #print response
        if len(response) > 0:
            for r in response:
                rr=cytoscape("network", "destroy",{"network":"SUID:"+str(r)},\
                             host=host, port=port)
    
    # String protein query
    query_genes=[ str(s) for s in query_genes ]

    response=cytoscape("string", "protein query",\
                      {"query":",".join(query_genes),\
                       "cutoff":str(cutoff),\
                       "species":species,\
                       "limit":str(limit),\
                       "taxonID":taxon},\
                       host=host, port=port)

    print("giving some time to cytoscape..")
    sys.stdout.flush()
    sleep(10)

    # apply new layout
    response=cytoscape("layout", "force-directed",\
                      {"defaultSpringCoefficient":".000004",\
                       "defaultSpringLength":"5"},\
                       host=host, port=port)
    
    # redefine defaults for node visualization
    response=loadTableData(df[["ensembl_gene_id","log2(fold_change)","NormInt","evidence"]].dropna(),\
                       df_key="ensembl_gene_id",table_key_column="query term",\
                      host=host, port=port)
    defaults_dic={"NODE_SHAPE":"ellipse",\
               "NODE_SIZE":60,\
               "NODE_FILL_COLOR":"#AAAAAA",\
               "EDGE_TRANSPARENCY":120}
    defaults_list=simple_defaults(defaults_dic)

    # apply mappings - blue / white / red - from -4 to +4 log2FC
    NODE_LABEL=mapVisualProperty("NODE_LABEL","passthrough","display name",host=host, port=port)

    create_styles("dataStyle",defaults_list,[NODE_LABEL],host=host, port=port)
    response=cytoscape("vizmap", "apply", {"styles":"dataStyle"},host=host, port=port)
    cmap = matplotlib.cm.get_cmap("bwr")
    norm = matplotlib.colors.Normalize(vmin=-4, vmax=4)
    min_color=matplotlib.colors.rgb2hex(cmap(norm(-4)))
    center_color=matplotlib.colors.rgb2hex(cmap(norm(0)))
    max_color=matplotlib.colors.rgb2hex(cmap(norm(4)))  

    NODE_FILL_COLOR=mapVisualProperty('NODE_FILL_COLOR','continuous','log2(fold_change)',\
                         lower=[-4,min_color],center=[0.0,center_color],upper=[4,max_color],\
                                     host=host, port=port)
    
    # apply diamond shape and increase node size to nodes with aging evidence
    NODE_SHAPE=mapVisualProperty('NODE_SHAPE','discrete','evidence',discrete=[ ["aging_gene","no"], ["DIAMOND", "ellipse"] ],\
                                host=host, port=port)
    NODE_SIZE=mapVisualProperty('NODE_SIZE','discrete','evidence',discrete=[ ["aging_gene","no"], ["100.0","60.0"] ],\
                               host=host, port=port)
    update_style("dataStyle",mappings=[NODE_SIZE,NODE_SHAPE,NODE_FILL_COLOR],\
                host=host, port=port)
    response=cytoscape("vizmap", "apply", {"styles":"dataStyle"},\
                      host=host, port=port)
    
    # apply mappings - reds - to Normalized expression (as in MA plots) to border color and border size
    NormIntDf = getTableColumns('node',['NormInt'],host=host, port=port)
    if 'NormInt' in NormIntDf.columns.tolist():
        min_NormInt = min(NormIntDf.dropna()['NormInt'].tolist())
        max_NormInt = max(NormIntDf.dropna()['NormInt'].tolist())
        cent_NormInt = np.mean([min_NormInt,max_NormInt])

        cmap = matplotlib.cm.get_cmap("Reds")
        norm = matplotlib.colors.Normalize(vmin=min_NormInt, vmax=max_NormInt)
        min_color=matplotlib.colors.rgb2hex(cmap(norm(np.mean([min_NormInt,max_NormInt]))))
        center_color=matplotlib.colors.rgb2hex(cmap(norm(cent_NormInt)))
        max_color=matplotlib.colors.rgb2hex(cmap(norm(max_NormInt)))  

        NODE_BORDER_PAINT=mapVisualProperty('NODE_BORDER_PAINT','continuous','NormInt',\
                             lower=[min_NormInt,min_color],center=[np.mean([min_NormInt,max_NormInt]),center_color],upper=[max_NormInt,max_color],\
                                           host=host, port=port)
        update_style("dataStyle",mappings=[NODE_BORDER_PAINT],\
                    host=host, port=port)
        response=cytoscape("vizmap", "apply", {"styles":"dataStyle"},\
                          host=host, port=port)

        NODE_BORDER_WIDTH=mapVisualProperty('NODE_BORDER_WIDTH','continuous','NormInt',\
                          lower=[min_NormInt,2],center=[np.mean([min_NormInt,max_NormInt]),4],upper=[max_NormInt,8],\
                                           host=host, port=port)
        update_style("dataStyle",mappings=[NODE_BORDER_WIDTH],\
                    host=host, port=port)
        response=cytoscape("vizmap", "apply", {"styles":"dataStyle"},\
                          host=host, port=port)

        response=cytoscape("network","rename",\
                           {"name":'main String network'},\
                          host=host, port=port)
    
    # create network with edges only
    response=cytoscape("network","select",\
                   {"edgeList":"all",\
                   "extendEdges":"true"},\
                  host=host, port=port)
    
    response=cytoscape("network","create",\
                   {"source":"current",\
                    "nodeList":"selected"},\
                  host=host, port=port)
    
    response=cytoscape("network","rename",\
                       {"name":'main String network (edges only)'},\
                      host=host, port=port)
    
    # top 10 changed genes > first neighbours

    response=cytoscape("network","set current",
                       {"network":"main String network (edges only)"},\
                      host=host, port=port)
    log2fcDf = getTableColumns('node',['log2(fold_change)'],host=host, port=port)
    if 'log2(fold_change)' in log2fcDf.columns.tolist():
        log2fcDf['log2(fold_change)']=log2fcDf['log2(fold_change)'].apply(lambda x: abs(x))
        log2fcDf=log2fcDf.sort_values(by=['log2(fold_change)'],ascending=False)
        top_nodes=log2fcDf.index.tolist()[:int(len(log2fcDf)*.10)]
        response=cytoscape("network","select",
                           {"nodeList":"name:"+",".join(top_nodes)},\
                          host=host, port=port)
        response=cytoscape("network","select",
                           {"firstNeighbors":"",\
                            "direction":"any",\
                            "network":"current"},\
                           host=host, port=port)
        response=cytoscape("network","create",
                           {"source":"current",\
                            "nodeList":"selected"},\
                          host=host, port=port)
        response=cytoscape("network","select",
                           {"edgeList":"all",\
                           "extendEdges":"true"},\
                          host=host, port=port)
        response=cytoscape("network","delete",
                           {"nodeList":"unselected"},\
                          host=host, port=port)
        response=cytoscape("network","deselect",{"edgeList":"all", "nodeList":"all"},\
                          host=host,port=port)
        response=cytoscape("layout", "force-directed",\
                          host=host, port=port)
        response=cytoscape("network","rename",\
                           {"name":'top '+str(int(len(log2fcDf)*.10))+' changed firstNeighbors'},\
                          host=host, port=port)
    
        #top 10 changed genes difusion
        response=cytoscape("network","set current",
                           {"network":"main String network (edges only)"},\
                          host=host, port=port)
        response=cytoscape("network","deselect",{"edgeList":"all", "nodeList":"all"},\
                          host=host, port=port)
        response=cytoscape("network","select",
                           {"nodeList":"name:"+",".join(top_nodes)},\
                          host=host, port=port)
        response=cytoscape("diffusion","diffuse",host=host, port=port)
        response=cytoscape("network","create",
                           {"source":"current",\
                          "nodeList":"selected"},\
                          host=host, port=port)
        response=cytoscape("network","select",
                           {"edgeList":"all",\
                           "extendEdges":"true"},\
                          host=host, port=port)
        response=cytoscape("network","delete",
                           {"nodeList":"unselected"},\
                          host=host, port=port)
        response=cytoscape("network","deselect",{"edgeList":"all", "nodeList":"all"},\
                          host=host, port=port)
        response=cytoscape("layout", "force-directed",host=host, port=port)
        response=cytoscape("network","rename",\
                           {"name":'top '+str(int(len(log2fcDf)*.10))+' changed diffusion'},\
                          host=host, port=port)
    
    def MAKETMP():
        (fd, f) = tempfile.mkstemp()
        f="/tmp/"+f.split("/")[-1]
        return f


    cys=MAKETMP()
    cyjs=MAKETMP()
    main_png=MAKETMP()
    main_pdf=MAKETMP()
    edg_png=MAKETMP()
    edg_pdf=MAKETMP()
    neig_png=MAKETMP()
    neig_pdf=MAKETMP()
    dif_png=MAKETMP()
    dif_pdf=MAKETMP()
    
    response=cytoscape("session", "save as" , \
                   {"file":cys},\
                 host=host, port=port)

    response=cytoscape("network", "export" , \
                       {"options":'CYJS',\
                        "OutputFile":cyjs},\
                      host=host, port=port)

    response=cytoscape("network","set current",
                       {"network":"main String network"},\
                      host=host, port=port)
    response=cytoscape("network","deselect",{"edgeList":"all", "nodeList":"all"},\
                      host=host, port=port)
    sleep(5)
    response=cytoscape("view", "export" , \
                       {"options":"PNG",\
                        "OutputFile":main_png},\
                      host=host, port=port)

    response=cytoscape("view", "export" , \
                       {"options":"PDF",\
                        "OutputFile":main_pdf},\
                      host=host, port=port)

    
    response=cytoscape("network","set current",
                   {"network":"main String network (edges only)"},\
                  host=host, port=port)
    response=cytoscape("network","deselect",{"edgeList":"all", "nodeList":"all"},\
                      host=host, port=port)
    sleep(5)
    response=cytoscape("view", "export" , \
                       {"options":"PNG",\
                        "OutputFile":edg_png},\
                      host=host, port=port)

    response=cytoscape("view", "export" , \
                       {"options":"PDF",\
                        "OutputFile":edg_pdf},\
                      host=host, port=port)
    

    try:
        response=cytoscape("network","set current",
                           {"network":'top '+str(int(len(log2fcDf)*.10))+' changed firstNeighbors'},\
                          host=host, port=port)
        response=cytoscape("network","deselect",{"edgeList":"all", "nodeList":"all"},\
                          host=host, port=port)
        sleep(5)

        response=cytoscape("view", "export" , \
                           {"options":"PNG",\
                            "OutputFile":neig_png},\
                          host=host, port=port)

        response=cytoscape("view", "export" , \
                           {"options":"PDF",\
                            "OutputFile":neig_pdf},\
                          host=host, port=port)
    except:
        print("No "+"changed firstNeighbors")
        sys.stdout.flush()

    try:
        response=cytoscape("network","set current",
                           {"network":'top '+str(int(len(log2fcDf)*.10))+' changed diffusion'},\
                          host=host, port=port)
        response=cytoscape("network","deselect",{"edgeList":"all", "nodeList":"all"},\
                          host=host, port=port)
        sleep(5)

        response=cytoscape("view", "export" , \
                           {"options":"PNG",\
                            "OutputFile":dif_png},\
                          host=host, port=port)

        response=cytoscape("view", "export" , \
                           {"options":"PDF",\
                            "OutputFile":dif_pdf},\
                          host=host, port=port)
    except:
        print("No "+"changed diffusion")
        sys.stdout.flush()    

    ssh = paramiko.SSHClient()
    ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
    ssh.connect(host)

    ftp_client=ssh.open_sftp()

    for f, extension, local in zip([cys,cyjs,main_png,main_pdf,edg_png,edg_pdf,neig_png,neig_pdf,dif_png,dif_pdf],\
                                    [".cys",".cyjs",".png",".pdf",".png",".pdf",".png",".pdf",".png",".pdf" ],\
                                    [target+".cys",target+".cyjs",target+".main.png",target+".main.pdf",\
                                    target+".main.edges.png",target+".main.edges.pdf",\
                                    target+".topFirstNeighbors.png",target+".topFirstNeighbors.pdf",\
                                    target+".topDiffusion.png",target+".topDiffusion.pdf"]):
        try:
            ftp_client.get(f+extension,local)
            ssh_stdin, ssh_stdout, ssh_stderr = ssh.exec_command("rm "+f+extension )
        except:
            print("No "+local)
            sys.stdout.flush()