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)
def draw_format_method(fmt, mth):
"""Render graphics format and method output."""
inputs = define_inputs()
outfilename = os.path.join(OUTDIR, "%s.%s" % (mth, fmt))
stem = "ANIm_percentage_identity"
df = pd.read_csv(inputs['infilename'], index_col=0, sep="\t")
os.makedirs(OUTDIR, exist_ok=True)
fn = {"mpl": pyani_graphics.heatmap_mpl,
"seaborn": pyani_graphics.heatmap_seaborn}
params = {"mpl": pyani_config.params_mpl,
"seaborn": pyani_config.params_mpl}
method_params = pyani_graphics.Params(params[mth](df)[stem],
inputs['labels'], inputs['classes'])
fn[mth](df, outfilename, title="%s:%s test" % (mth, fmt),
params=method_params)
def draw_format_method(fmt, mth):
"""Render graphics format and method output."""
inputs = define_inputs()
outfilename = OUTDIR / f"{mth}.{fmt}"
stem = "ANIm_percentage_identity"
df = pd.read_csv(inputs["infilename"], index_col=0, sep="\t")
OUTDIR.mkdir(exist_ok=True)
fn = {
"mpl": pyani_graphics.mpl.heatmap,
"seaborn": pyani_graphics.sns.heatmap
}
params = {
"mpl": pyani_config.params_mpl,
"seaborn": pyani_config.params_mpl
}
method_params = pyani_graphics.Params(params[mth](df)[stem],
inputs["labels"], inputs["classes"])
fn[mth](df, outfilename, title=f"{mth}:{fmt} test", params=method_params)
def draw_format_method(fmt, mth, graphics_inputs, tmp_path):
"""Render graphics format and method output."""
df = pd.read_csv(graphics_inputs.filename, index_col=0, sep="\t")
fn = {
"mpl": pyani_graphics.mpl.heatmap,
"seaborn": pyani_graphics.sns.heatmap
}
params = {
"mpl": pyani_config.params_mpl,
"seaborn": pyani_config.params_mpl
}
method_params = pyani_graphics.Params(
params[mth](df)["ANIm_percentage_identity"],
graphics_inputs.labels,
graphics_inputs.classes,
)
fn[mth](df,
tmp_path / f"{mth}.{fmt}",
title=f"{mth}:{fmt} test",
params=method_params)
def write_heatmap(
run_id: int,
matdata: MatrixData,
result_labels: Dict,
result_classes: Dict,
outfmts: List[str],
args: Namespace,
logger: Logger,
) -> None:
"""Write a single heatmap for a pyani run.
:param run_id: int, run_id for this run
:param matdata: MatrixData object for this heatmap
:param result_labels: dict of result labels
:param result_classes: dict of result classes
:param args: Namespace for command-line arguments
:param outfmts: list of output formats for files
:param logger: logging object
"""
logger.info(f"Writing {matdata.name} matrix heatmaps")
cmap = pyani_config.get_colormap(matdata.data, matdata.name)
for fmt in outfmts:
outfname = Path(
args.outdir) / f"matrix_{matdata.name}_run{run_id}.{fmt}"
logger.info(f"\tWriting graphics to {outfname}")
params = pyani_graphics.Params(cmap, result_labels, result_classes)
# Draw heatmap
GMETHODS[args.method](
matdata.data,
outfname,
title=f"matrix_{matdata.name}_run{run_id}",
params=params,
)
# Be tidy with matplotlib caches
plt.close("all")
