def draw(filestems, gformat, logger=None):
"""Draw ANIb/ANIm/TETRA results
- filestems - filestems for output files
- gformat - the format for output graphics
"""
# Draw heatmaps
for filestem in filestems:
fullstem = os.path.join(args.outdirname, filestem)
outfilename = fullstem + '.%s' % gformat
infilename = fullstem + '.tab'
df = pd.read_csv(infilename, index_col=0, sep="\t")
if logger:
logger.info("Writing heatmap to %s", outfilename)
params = pyani_graphics.Params(
params_mpl(df)[filestem], pyani_tools.get_labels(args.labels),
pyani_tools.get_labels(args.classes))
if args.gmethod == "mpl":
pyani_graphics.heatmap_mpl(df,
outfilename=outfilename,
title=filestem,
params=params)
elif args.gmethod == "seaborn":
pyani_graphics.heatmap_seaborn(df,
outfilename=outfilename,
title=filestem,
params=params)
def graphics_inputs(dir_graphics_in):
"""Returns namedtuple of graphics inputs."""
return GraphicsTestInputs(
dir_graphics_in / "ANIm_percentage_identity.tab",
get_labels(dir_graphics_in / "labels.tab"),
get_labels(dir_graphics_in / "classes.tab"),
)
def draw(args: Namespace, filestems: List[str], gformat: str) -> None:
"""Draw ANIb/ANIm/TETRA results.
:param args: Namespace, command-line arguments
:param logger: logging object
:param filestems: - filestems for output files
:param gformat: - the format for output graphics
"""
logger = logging.getLogger(__name__)
# Draw heatmaps
for filestem in filestems:
fullstem = args.outdirname / filestem
outfilename = fullstem.with_suffix(".%s" % gformat)
infilename = fullstem.with_suffix(".tab")
dfm = pd.read_csv(infilename, index_col=0, sep="\t")
logger.info("Writing heatmap to %s", outfilename)
print(args.labels, args.classes)
params = pyani_graphics.Params(
params_mpl(dfm)[filestem],
pyani_tools.get_labels(args.labels, logger=logger),
pyani_tools.get_labels(args.classes, logger=logger),
)
if args.gmethod == "mpl":
pyani_graphics.mpl.heatmap(dfm,
outfilename=outfilename,
title=filestem,
params=params)
elif args.gmethod == "seaborn":
pyani_graphics.sns.heatmap(dfm,
outfilename=outfilename,
title=filestem,
params=params)
def define_inputs():
return {'infilename': os.path.join("tests", "target_ANIm_output",
"ANIm_percentage_identity.tab"),
'labels': pyani_tools.get_labels(os.path.join("tests",
"test_ani_data",
"labels.tab"),
logger=None),
'classes': pyani_tools.get_labels(os.path.join("tests",
"test_ani_data",
"classes.tab"),
logger=None)}
def define_inputs():
"""Return a dict of input files, keyed by file name option."""
return {
"infilename":
TESTDIR / "target_ANIm_output" / "ANIm_percentage_identity.tab",
"labels":
pyani_tools.get_labels(TESTDIR / "test_ani_data" / "labels.tab",
logger=None),
"classes":
pyani_tools.get_labels(TESTDIR / "test_ani_data" / "classes.tab",
logger=None),
}