def main(args=None):
args = parse_arguments().parse_args(args)
corr = Correlation(args.corData,
labels=args.labels,)
args.plotFile.close()
corr.rowCenter = args.rowCenter
corr.plot_pca(args.plotFile.name,
plot_title=args.plotTitle,
image_format=args.plotFileFormat)
if args.outFileNameData is not None:
import matplotlib
mlab_pca = matplotlib.mlab.PCA(corr.matrix)
n = len(corr.labels)
of = args.outFileNameData
of.write("Component\t{}\tEigenvalue\n".format("\t".join(corr.labels)))
for i in range(n):
of.write("{}".format(i + 1))
for v in mlab_pca.Wt[i, :]:
of.write("\t{}".format(v))
of.write("\t{}\n".format(mlab_pca.s[i]))
args.outFileNameData.close()
def main(args=None):
args = parse_arguments().parse_args(args)
corr = Correlation(
args.corData,
labels=args.labels,
)
args.plotFile.close()
corr.rowCenter = args.rowCenter
corr.plot_pca(args.plotFile.name,
plot_title=args.plotTitle,
image_format=args.plotFileFormat)
if args.outFileNameData is not None:
import matplotlib
mlab_pca = matplotlib.mlab.PCA(corr.matrix)
n = len(corr.labels)
of = args.outFileNameData
of.write("Component\t{}\tEigenvalue\n".format("\t".join(corr.labels)))
for i in range(n):
of.write("{}".format(i + 1))
for v in mlab_pca.Wt[i, :]:
of.write("\t{}".format(v))
of.write("\t{}\n".format(mlab_pca.s[i]))
args.outFileNameData.close()
def main(args=None):
args = parse_arguments().parse_args(args)
if args.plotFile is None and args.outFileNameData is None:
sys.exit(
"At least one of --plotFile and --outFileNameData must be specified!\n"
)
if args.ntop < 0:
sys.exit("The value specified for --ntop must be >= 0!\n")
if args.PCs[0] == args.PCs[1]:
sys.exit("You must specify different principal components!\n")
if args.PCs[0] <= 0 or args.PCs[1] <= 0:
sys.exit("The specified principal components must be at least 1!\n")
corr = Correlation(
args.corData,
labels=args.labels,
)
corr.rowCenter = args.rowCenter
corr.transpose = args.transpose
corr.ntop = args.ntop
corr.log2 = args.log2
Wt, eigenvalues = corr.plot_pca(args.plotFile,
PCs=args.PCs,
plot_title=args.plotTitle,
image_format=args.plotFileFormat,
plotWidth=args.plotWidth,
plotHeight=args.plotHeight,
cols=args.colors,
marks=args.markers)
if args.outFileNameData is not None:
of = open(args.outFileNameData, "w")
of.write("#plotPCA --outFileNameData\n")
of.write("Component\t{}\tEigenvalue\n".format("\t".join(corr.labels)))
n = eigenvalues.shape[0]
for i in range(n):
of.write("{}\t{}\t{}\n".format(
i + 1, "\t".join(["{}".format(x) for x in Wt[i, :]]),
eigenvalues[i]))
of.close()
def main(args=None):
args = parse_arguments().parse_args(args)
if args.plotFile is None and args.outFileNameData is None:
sys.exit("At least one of --plotFile and --outFileNameData must be specified!\n")
if args.ntop < 0:
sys.exit("The value specified for --ntop must be >= 0!\n")
if args.PCs[0] == args.PCs[1]:
sys.exit("You must specify different principal components!\n")
if args.PCs[0] <= 0 or args.PCs[1] <= 0:
sys.exit("The specified principal components must be at least 1!\n")
corr = Correlation(args.corData,
labels=args.labels,)
corr.rowCenter = args.rowCenter
corr.transpose = args.transpose
corr.ntop = args.ntop
corr.log2 = args.log2
Wt, eigenvalues = corr.plot_pca(args.plotFile,
PCs=args.PCs,
plot_title=args.plotTitle,
image_format=args.plotFileFormat,
plotWidth=args.plotWidth,
plotHeight=args.plotHeight,
cols=args.colors,
marks=args.markers)
if args.outFileNameData is not None:
of = open(args.outFileNameData, "w")
of.write("#plotPCA --outFileNameData\n")
of.write("Component\t{}\tEigenvalue\n".format("\t".join(corr.labels)))
n = eigenvalues.shape[0]
for i in range(n):
of.write("{}\t{}\t{}\n".format(i + 1, "\t".join(["{}".format(x) for x in Wt[i, :]]), eigenvalues[i]))
of.close()