def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-t", "--test", dest="test", type="string",
help="supply help")
parser.add_option("--plot-type", dest="plot_type", type="choice",
choices=["histogram", "scatter", "barchart"],
help="type of plot to generate")
parser.add_option("--x-axis", dest="x_axis", type="string",
help="variable to plot on the X-axis."
"This is the default axis for plotting.")
parser.add_option("--y-axis", dest="y_axis", type="string",
help="variable to plot on the Y-axis")
parser.add_option("--split-by", dest="split_by", type="string",
help="varible over which to split up plots")
parser.add_option("--X-title", dest="x_title", type="string",
help="label to attach to X-axis")
parser.add_option("--Y-title", dest="y_title", type="string",
help="label to attach to Y-axis")
parser.add_option("--colour-var", dest="col_var", type="string",
help="variable to colour points by")
parser.add_option("--free-scale", dest="free_scale", type="choice",
choices=["free_x", "free_y", "free"], help="whether to "
"use free scaling on plot axes")
parser.add_option("--outfile", dest="outfile", type="string",
help="file to save plot to")
parser.add_option("--melt-data", dest="melt", action="store_true",
help="melt the dataframe first, requires ID vars")
parser.add_option("--melt-id-vars", dest="id_vars", type="string",
help="comma separated list of id variables for"
" the melted dataframe")
parser.add_option("--merge-frames", dest="merge", action="store_true",
help="merge two input dataframes together")
parser.add_option("--merge-id-vars", dest="merge_vars", type="string",
help="comma separate list of id variables to merge "
"two dataframes on")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
parser.set_defaults(free_scale="both",
split_by=None,
col_var=None,
melt=False)
infile = argv[-1]
if len(infile.split(",")) == 2:
infiles = infile.split(",")
df1 = pd.read_table(infiles[0], sep=":", index_col=0,
header=0)
df2 = pd.read_table(infiles[1], sep=":", index_col=0,
header=0)
ids = options.merge_vars.split(",")
df1[options.y_axis] = df1.index
df2[options.y_axis] = df2.index
df1.columns = [ids[0], options.y_axis]
df2.columns = [ids[0], options.y_axis]
df = pd.merge(df1, df2, on=options.y_axis)
# these need to not be hard-coded!
df.columns = ["mean_h2", ids[0], "fano_h2"]
else:
df = pd.read_table(infile, sep="\t", index_col=0,
header=0)
# assumes the first column is the index
if options.melt:
mids = options.id_vars.split(",")
if options.y_axis:
_df = pd.melt(df, id_vars=options.x_axis, value_name=options.y_axis,
var_name=options.col_var)
else:
_df = pd.melt(df, id_vars=mids, value_name=options.x_axis,
var_name=options.col_var)
df = _df
else:
pass
# check variables are present
try:
var = df[options.x_axis]
except ValueError:
raise ValueError("no plotting variable found")
if options.col_var:
try:
cols = df[options.col_var]
except ValueError:
E.warn("Colour variable not found in data frame."
"Check the data file is the correct one")
else:
pass
if options.split_by:
try:
splits = df[options.split_by]
except ValueError:
E.warn("Split-by variable not found in the data "
"frame. Check the data file is the correct"
" one.")
else:
pass
try:
assert options.outfile
except AssertionError:
raise IOError("no output file detected")
if options.plot_type == "histogram":
P52.plotHistogram(data=df,
variable=options.x_axis,
save_path=options.outfile,
x_title=options.x_title,
y_title=options.y_title,
colour_var=options.col_var,
scales=options.free_scale,
split_var=options.split_by)
elif options.plot_type == "barchart":
P52.plotBarchart(data=df,
x_variable=options.x_axis,
y_variable=options.y_axis,
save_path=options.outfile,
x_title=options.x_title,
y_title=options.y_title,
colour_var=options.col_var,
split_var=options.split_by)
else:
pass
# write footer and output benchmark information.
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-t",
"--test",
dest="test",
type="string",
help="supply help")
parser.add_option("--plot-type",
dest="plot_type",
type="choice",
choices=["histogram", "scatter", "barchart"],
help="type of plot to generate")
parser.add_option("--x-axis",
dest="x_axis",
type="string",
help="variable to plot on the X-axis."
"This is the default axis for plotting.")
parser.add_option("--y-axis",
dest="y_axis",
type="string",
help="variable to plot on the Y-axis")
parser.add_option("--split-by",
dest="split_by",
type="string",
help="varible over which to split up plots")
parser.add_option("--X-title",
dest="x_title",
type="string",
help="label to attach to X-axis")
parser.add_option("--Y-title",
dest="y_title",
type="string",
help="label to attach to Y-axis")
parser.add_option("--colour-var",
dest="col_var",
type="string",
help="variable to colour points by")
parser.add_option("--free-scale",
dest="free_scale",
type="choice",
choices=["free_x", "free_y", "free"],
help="whether to "
"use free scaling on plot axes")
parser.add_option("--outfile",
dest="outfile",
type="string",
help="file to save plot to")
parser.add_option("--melt-data",
dest="melt",
action="store_true",
help="melt the dataframe first, requires ID vars")
parser.add_option("--melt-id-vars",
dest="id_vars",
type="string",
help="comma separated list of id variables for"
" the melted dataframe")
parser.add_option("--merge-frames",
dest="merge",
action="store_true",
help="merge two input dataframes together")
parser.add_option("--merge-id-vars",
dest="merge_vars",
type="string",
help="comma separate list of id variables to merge "
"two dataframes on")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
parser.set_defaults(free_scale="both",
split_by=None,
col_var=None,
melt=False)
infile = argv[-1]
if len(infile.split(",")) == 2:
infiles = infile.split(",")
df1 = pd.read_table(infiles[0], sep=":", index_col=0, header=0)
df2 = pd.read_table(infiles[1], sep=":", index_col=0, header=0)
ids = options.merge_vars.split(",")
df1[options.y_axis] = df1.index
df2[options.y_axis] = df2.index
df1.columns = [ids[0], options.y_axis]
df2.columns = [ids[0], options.y_axis]
df = pd.merge(df1, df2, on=options.y_axis)
# these need to not be hard-coded!
df.columns = ["mean_h2", ids[0], "fano_h2"]
else:
df = pd.read_table(infile, sep="\t", index_col=0, header=0)
# assumes the first column is the index
if options.melt:
mids = options.id_vars.split(",")
if options.y_axis:
_df = pd.melt(df,
id_vars=options.x_axis,
value_name=options.y_axis,
var_name=options.col_var)
else:
_df = pd.melt(df,
id_vars=mids,
value_name=options.x_axis,
var_name=options.col_var)
df = _df
else:
pass
# check variables are present
try:
var = df[options.x_axis]
except ValueError:
raise ValueError("no plotting variable found")
if options.col_var:
try:
cols = df[options.col_var]
except ValueError:
E.warn("Colour variable not found in data frame."
"Check the data file is the correct one")
else:
pass
if options.split_by:
try:
splits = df[options.split_by]
except ValueError:
E.warn("Split-by variable not found in the data "
"frame. Check the data file is the correct"
" one.")
else:
pass
try:
assert options.outfile
except AssertionError:
raise IOError("no output file detected")
if options.plot_type == "histogram":
P52.plotHistogram(data=df,
variable=options.x_axis,
save_path=options.outfile,
x_title=options.x_title,
y_title=options.y_title,
colour_var=options.col_var,
scales=options.free_scale,
split_var=options.split_by)
elif options.plot_type == "barchart":
P52.plotBarchart(data=df,
x_variable=options.x_axis,
y_variable=options.y_axis,
save_path=options.outfile,
x_title=options.x_title,
y_title=options.y_title,
colour_var=options.col_var,
split_var=options.split_by)
else:
pass
# write footer and output benchmark information.
E.Stop()
