Commit ⋅ widdowquinn/pyani

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pyani/pyani_graphics/sns/__init__.py changed.

pyani/scripts/subcommands/subcmd_plot.py changed.

@@ -161,7 +161,7 @@

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# Generate Seaborn heatmap output
def heatmap(dfr, outfilename=None, title=None, params=None, args=None):
def heatmap(dfr, outfilename=None, title=None, format=None, params=None, args=None):
    """Return seaborn heatmap with cluster dendrograms.

    :param dfr:  pandas DataFrame with relevant data

@@ -198,7 +198,7 @@

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    # Tree
    newicks = None
    if args.tree:
        newicks = tree(dfr, fig, outfilename, title, params, args)
        newicks = tree(dfr, fig, title, format, params, args)

    # Return clustermap
    return fig, newicks

@@ -328,22 +328,23 @@

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        return newick


def tree(dfr, fig, matfname, mat_title, params, args):
def tree(dfr, fig, title, format, params, args):
    """Generate a newick file and dendrogram plot for the given dataframe.

    :param dfr:  a dataframe
    :param fig:  a figure produced by sns.clustermap
    :param matfname:  name of the matrix plot file
    :param title:  name of the matrix plot
    :param format:  image file format being used
    :param params:  matrix plot parameters; including labels
    :param args:  Namespace

    """
    logger = logging.getLogger(__name__)
    # The header row must start with '#Names' for ClusterTree()'s text_array parameter to be satisfied
    # Create a text stream with the dataframe contents in the necessary format for ClusterTree
    # dfr.index.name = "#Names"
    # matrix = dfr.to_csv(None, sep="\t", header=True)

    # Get matrix name and run_id from the plot title
    matname, run_id = title.split("_", 1)[-1].rsplit("_", 1)

    # Dictionary to allow abstraction over axes
    sides = {
        "col": {
            "axis": fig.dendrogram_col,

@@ -356,18 +357,14 @@

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    }

    # Create a linkage dendrogram and newick string for both rows and columns
    # newicks = {}
    newicks = {}

    for axis in sides.keys():
        # Generate newick format
        tree = hierarchy.to_tree(sides[axis]["axis"].linkage, False)
        logger.debug(f"Names: {sides[axis]['names']}")
        newick = get_newick(tree, tree.dist, sides[axis]["names"], "")
        newick_file = Path(args.outdir) / str(
            mat_title.replace("matrix", f"{axis}_newick") + ".nw"
        )

        # newicks.update({axis: newick})
        newicks.update({f"[{axis}_newick_{matname}_{run_id}]": newick})

        # Generate dendrogram
        # if 'dendrogram' in args.tree:

@@ -376,14 +373,12 @@

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        # figtree = ClusterTree(newick, text_array=matrix)
        figtree = PhyloTree(newick)
        figtree.set_species_naming_function(get_species_name)
        figtree_file = str(matfname).replace("matrix", f"{axis}_tree")
        figtree_file = Path(args.outdir) / f"{axis}_tree_{matname}_{run_id}.{format}"
        logger.debug(f"{figtree}")
        figtree.render(figtree_file, layout=tree_layout)
        # with open(newick_file, 'w') as ofh:
        figtree.write(outfile=newick_file)
        figtree.render(str(figtree_file), layout=tree_layout)

    # Return the newick strings so we can save them in the database (eventually)
    # return newicks
    return newicks


def tree_layout(node):

@@ -55,12 +55,15 @@

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# Distribution dictionary of matrix graphics methods
GMETHODS = {"mpl": pyani_graphics.mpl.heatmap, "seaborn": pyani_graphics.sns.heatmap}
SMETHODS = {"mpl": pyani_graphics.mpl.scatter, "seaborn": pyani_graphics.sns.scatter}
# TMETHODS = {"seaborn": pyani_graphics.seaborn.}
# Distribution dictionary of distribution graphics methods
DISTMETHODS = {
    "mpl": pyani_graphics.mpl.distribution,
    "seaborn": pyani_graphics.sns.distribution,
}

NEWICKS = {}


def subcmd_plot(args: Namespace) -> int:
    """Produce graphical output for an analysis.

@@ -92,6 +95,10 @@

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    for run_id in run_ids:
        write_run_heatmaps(run_id, session, outfmts, args)

        if NEWICKS:
            write_newicks(args, run_id)
        NEWICKS.clear()

    return 0



@@ -197,16 +204,22 @@

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        logger.debug("\tWriting graphics to %s", outfname)
        params = pyani_graphics.Params(cmap, result_labels, result_classes)
        # Draw heatmap
        GMETHODS[args.method](
        _, newicks = GMETHODS[args.method](
            matdata.data,
            outfname,
            title=f"matrix_{matdata.name}_run{run_id}",
            format=fmt,
            params=params,
            args=args,
        )

    # If Newick strings were generated, add them to NEWICKS.
    if newicks:
        NEWICKS.update(newicks)

    # Be tidy with matplotlib caches
    plt.close("all")
    return


def write_scatter(

@@ -252,3 +265,11 @@

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252	265
253	266		# Be tidy with matplotlib caches
254	267		plt.close("all")
	268	+
	269	+
	270	+	def write_newicks(args: Namespace, run_id):
	271	+	# If Newick strings were generated, write them out.
	272	+	newick_file = Path(args.outdir) / f"newicks_run{run_id}.nw"
	273	+	with open(newick_file, "w") as nfh:
	274	+	for name, nw in NEWICKS.items():
	275	+	nfh.write(f"{name}\t{nw}\n")

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  range: 70...100

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  layout: "header, diff"
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161	161
162	162
163	163		# Generate Seaborn heatmap output
164		-	def heatmap(dfr, outfilename=None, title=None, params=None, args=None):
	164	+	def heatmap(dfr, outfilename=None, title=None, format=None, params=None, args=None):
165	165		"""Return seaborn heatmap with cluster dendrograms.
166	166
167	167		:param dfr: pandas DataFrame with relevant data

328	328		return newick
329	329
330	330
331		-	def tree(dfr, fig, matfname, mat_title, params, args):
	331	+	def tree(dfr, fig, title, format, params, args):
332	332		"""Generate a newick file and dendrogram plot for the given dataframe.
333	333
334	334		:param dfr: a dataframe
335	335		:param fig: a figure produced by sns.clustermap
336		-	:param matfname: name of the matrix plot file
	336	+	:param title: name of the matrix plot
	337	+	:param format: image file format being used
337	338		:param params: matrix plot parameters; including labels
338	339		:param args: Namespace
339	340
340	341		"""
341	342		logger = logging.getLogger(__name__)
342		-	# The header row must start with '#Names' for ClusterTree()'s text_array parameter to be satisfied
343		-	# Create a text stream with the dataframe contents in the necessary format for ClusterTree
344		-	# dfr.index.name = "#Names"
345		-	# matrix = dfr.to_csv(None, sep="\t", header=True)
346	343
	344	+	# Get matrix name and run_id from the plot title
	345	+	matname, run_id = title.split("_", 1)[-1].rsplit("_", 1)
	346	+
	347	+	# Dictionary to allow abstraction over axes
347	348		sides = {
348	349		"col": {
349	350		"axis": fig.dendrogram_col,

356	357		}
357	358
358	359		# Create a linkage dendrogram and newick string for both rows and columns
359		-	# newicks = {}
	360	+	newicks = {}
360	361
361	362		for axis in sides.keys():
362	363		# Generate newick format
363	364		tree = hierarchy.to_tree(sides[axis]["axis"].linkage, False)
364	365		logger.debug(f"Names: {sides[axis]['names']}")
365	366		newick = get_newick(tree, tree.dist, sides[axis]["names"], "")
366		-	newick_file = Path(args.outdir) / str(
367		-	mat_title.replace("matrix", f"{axis}_newick") + ".nw"
368		-	)
369		-
370		-	# newicks.update({axis: newick})
	367	+	newicks.update({f"[{axis}_newick_{matname}_{run_id}]": newick})
371	368
372	369		# Generate dendrogram
373	370		# if 'dendrogram' in args.tree:

376	373		# figtree = ClusterTree(newick, text_array=matrix)
377	374		figtree = PhyloTree(newick)
378	375		figtree.set_species_naming_function(get_species_name)
379		-	figtree_file = str(matfname).replace("matrix", f"{axis}_tree")
	376	+	figtree_file = Path(args.outdir) / f"{axis}_tree_{matname}_{run_id}.{format}"
380	377		logger.debug(f"{figtree}")
381		-	figtree.render(figtree_file, layout=tree_layout)
382		-	# with open(newick_file, 'w') as ofh:
383		-	figtree.write(outfile=newick_file)
	378	+	figtree.render(str(figtree_file), layout=tree_layout)
384	379
385	380		# Return the newick strings so we can save them in the database (eventually)
386		-	# return newicks
	381	+	return newicks
387	382
388	383
389	384		def tree_layout(node):

197	204		logger.debug("\tWriting graphics to %s", outfname)
198	205		params = pyani_graphics.Params(cmap, result_labels, result_classes)
199	206		# Draw heatmap
200		-	GMETHODS[args.method](
	207	+	_, newicks = GMETHODS[args.method](
201	208		matdata.data,
202	209		outfname,
203	210		title=f"matrix_{matdata.name}_run{run_id}",
	211	+	format=fmt,
204	212		params=params,
205	213		args=args,
206	214		)
207	215
	216	+	# If Newick strings were generated, add them to NEWICKS.
	217	+	if newicks:
	218	+	NEWICKS.update(newicks)
	219	+
208	220		# Be tidy with matplotlib caches
209	221		plt.close("all")
	222	+	return
210	223
211	224
212	225		def write_scatter(

198	198		# Tree
199	199		newicks = None
200	200		if args.tree:
201		-	newicks = tree(dfr, fig, outfilename, title, params, args)
	201	+	newicks = tree(dfr, fig, title, format, params, args)
202	202
203	203		# Return clustermap
204	204		return fig, newicks

55	55		# Distribution dictionary of matrix graphics methods
56	56		GMETHODS = {"mpl": pyani_graphics.mpl.heatmap, "seaborn": pyani_graphics.sns.heatmap}
57	57		SMETHODS = {"mpl": pyani_graphics.mpl.scatter, "seaborn": pyani_graphics.sns.scatter}
	58	+	# TMETHODS = {"seaborn": pyani_graphics.seaborn.}
58	59		# Distribution dictionary of distribution graphics methods
59	60		DISTMETHODS = {
60	61		"mpl": pyani_graphics.mpl.distribution,
61	62		"seaborn": pyani_graphics.sns.distribution,
62	63		}
63	64
	65	+	NEWICKS = {}
	66	+
64	67
65	68		def subcmd_plot(args: Namespace) -> int:
66	69		"""Produce graphical output for an analysis.

92	95		for run_id in run_ids:
93	96		write_run_heatmaps(run_id, session, outfmts, args)
94	97
	98	+	if NEWICKS:
	99	+	write_newicks(args, run_id)
	100	+	NEWICKS.clear()
	101	+
95	102		return 0
96	103
97	104

1	#
2	# This codecov.yml is the default configuration for
3	# all repositories on Codecov. You may adjust the settings
4	# below in your own codecov.yml in your repository.
5	#
6	coverage:
7	precision: 2
8	round: down
9	range: 70...100
10
11	status:
12	# Learn more at https://docs.codecov.io/docs/commit-status
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14	patch: true
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17	comment:
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