def draw(results, filestems):
"""Draw ANIb/ANIm/TETRA results
- results - tuple of dataframes from ANIb analysis
"""
# Draw heatmaps
for df, filestem in zip(results, filestems):
fullstem = os.path.join(args.outdirname, filestem)
outfilename = fullstem + '.%s' % args.gformat
infilename = fullstem + '.tab'
logger.info("Writing heatmap to %s" % outfilename)
if args.gmethod == "mpl":
pyani_graphics.heatmap_mpl(df,
outfilename=outfilename,
title=filestem,
cmap=params_mpl(df)[filestem][0],
vmin=params_mpl(df)[filestem][1],
vmax=params_mpl(df)[filestem][2],
labels=get_labels(args.labels),
classes=get_labels(args.classes))
elif args.gmethod == "R":
rstr = pyani_graphics.heatmap_r(infilename,
outfilename,
gformat=args.gformat.lower(),
title=filestem,
cmap=params_r(df)[filestem][0],
vmin=params_r(df)[filestem][1],
vmax=params_r(df)[filestem][2],
labels=get_labels(args.labels),
classes=get_labels(args.classes))
logger.info("Executed R code:\n%s" % rstr)
def draw(results, filestems, gformat):
"""Draw ANIb/ANIm/TETRA results
- results - tuple of dataframes from ANIb analysis
"""
# Draw heatmaps
for df, filestem in zip(results, filestems):
fullstem = os.path.join(args.outdirname, filestem)
outfilename = fullstem + '.%s' % gformat
infilename = fullstem + '.tab'
logger.info("Writing heatmap to %s" % outfilename)
if args.gmethod == "mpl":
pyani_graphics.heatmap_mpl(df, outfilename=outfilename,
title=filestem,
cmap=params_mpl(df)[filestem][0],
vmin=params_mpl(df)[filestem][1],
vmax=params_mpl(df)[filestem][2],
labels=get_labels(args.labels),
classes=get_labels(args.classes))
elif args.gmethod == "R":
rstr = pyani_graphics.heatmap_r(infilename, outfilename,
gformat=gformat.lower(),
title=filestem,
cmap=params_r(df)[filestem][0],
vmin=params_r(df)[filestem][1],
vmax=params_r(df)[filestem][2],
labels=get_labels(args.labels),
classes=get_labels(args.classes))
logger.info("Executed R code:\n%s" % rstr)
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 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)
