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@@ -19,8 +19,8 @@ def cluster(dcmat, method, nclusters):
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"""
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lmat = squareform(dcmat)
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lobj = linkage(lmat, method = method)
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- clabs = [x + 1 for x in range(numclusts)]
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- clusts = fcluster(lobj, numclusts, criterion='maxclust')
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+ clabs = [x + 1 for x in range(nclusters)]
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+ clusts = fcluster(lobj, nclusters, criterion='maxclust')
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clustdf = p.DataFrame({'icp_id' : dcmat.index.values, 'cluster' : clusts})
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return lobj, clustdf
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@@ -55,12 +55,12 @@ def dendro(lobj, clustdf, numclusts, icps, fname):
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def main():
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parser = ArgumentParser(description='Cluster from pre-existing distance correlation matrix in pickled dataframe')
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- parser.add_argument("-i", "--input", dest="input", help = "input pickle path; default: ../data/5kdcorrmatrix.pkl", metavar="[PATH]", default = "../data/5kdcorrmatrix.pkl")
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- parser.add_argument("-o", "--output", dest="output", help = "output pickle path; default: ../data/5kdclustable.pkl", metavar="[PATH]", default = "../data/5kdclustable.pkl")
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- parser.add_argument("--method", dest="method", help = "clustering method; default 'ward'", metavar = "[METHOD]", default = "ward")
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- parser.add_argument("--clusters", dest="numclusters", help = "number of clusters; default: 9", metavar = "[NUM]", default = 9, type = int)
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+ parser.add_argument("-i", "--input", dest="input", help = "input pickle path; default: ../data/5kdcorrmatrix.pkl", metavar="PATH", default = "../data/5kdcorrmatrix.pkl")
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+ parser.add_argument("-o", "--output", dest="output", help = "output pickle path; default: ../data/5kdclustable.pkl", metavar="PATH", default = "../data/5kdclustable.pkl")
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+ parser.add_argument("--method", dest="method", help = "clustering method; default 'ward'", metavar = "METHOD", default = "ward")
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+ parser.add_argument("--clusters", dest="numclusters", help = "number of clusters; default: 9", metavar = "NUM", default = 9, type = int)
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parser.add_argument("-d", "--dendrogram", dest = "incdendro", help = "draw dendrogram", action ="store_true")
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- parser.add_argument("-t", "--tree", dest="treepath", help="Filename for dendrogram (if -d), default: ../img/59-9-dendro.png", metavar="[PATH]", default = "../img/5k-9-dendro.png")
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+ parser.add_argument("-t", "--tree", dest="treepath", help="Filename for dendrogram (if -d), default: ../img/59-9-dendro.png", metavar="PATH", default = "../img/5k-9-dendro.png")
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args = parser.parse_args()
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print("Clustering")
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