some progress made

src/sourmash/cli/plot.py

@@ -10,16 +10,24 @@ def subparser(subparsers):
         help='output PDF; default is PNG'
     )
     subparser.add_argument(
-        '--labels', action='store_true',
+        '--labels', action='store_true', default=False,
         help='show sample labels on dendrogram/matrix'
     )
+    subparser.add_argument(
+        '--no-labels', action='store_false', dest='labels',
+        help='do not show sample labels'
+    )
     subparser.add_argument(
         '--labeltext',
-        help='filename containing list of labels (overrides signature names)'
+        help='filename containing list of labels (overrides signature names); implies --labels'
+    )
+    subparser.add_argument(
+        '--indices', action='store_true', default=True,
+        help='show sample indices but not labels; overridden by --labels'
     )
     subparser.add_argument(
-        '--indices', action='store_false',
-        help='show sample indices but not labels'
+        '--no-indices', action='store_false', dest='indices',
+        help='do not show sample indices'
     )
     subparser.add_argument(
         '--vmin', default=0.0, type=float,

src/sourmash/commands.py

@@ -246,20 +246,33 @@ def plot(args):
 
     # load files
     D_filename = args.distances
-    labelfilename = D_filename + '.labels.txt'
 
     notify(f'loading comparison matrix from {D_filename}...')
     D = numpy.load(open(D_filename, 'rb'))
     # not sure how to change this to use f-strings
     notify('...got {} x {} matrix.', *D.shape)
 
-    if args.labeltext:
-        labelfilename = args.labeltext
-    notify(f'loading labels from {labelfilename}')
-    labeltext = [ x.strip() for x in open(labelfilename) ]
-    if len(labeltext) != D.shape[0]:
-        error('{} labels != matrix size, exiting', len(labeltext))
-        sys.exit(-1)
+    if args.labels or args.labeltext:
+        args.labels = True
+        if args.labeltext:
+            labelfilename = args.labeltext
+        else:
+            labelfilename = D_filename + '.labels.txt'
+
+        notify(f'loading labels from {labelfilename}')
+        labeltext = [ x.strip() for x in open(labelfilename) ]
+
+        if len(labeltext) != D.shape[0]:
+            error('{} labels != matrix size, exiting', len(labeltext))
+            sys.exit(-1)
+    elif args.indices:
+        # construct integer labels
+        labeltext = [str(i) for i in range(D.shape[0])]
+        args.labels = True
+    else:
+        assert not args.labels
+        assert not args.indices
+        assert not args.labeltext
 
     # build filenames, decide on PDF/PNG output
     dendrogram_out = os.path.basename(D_filename) + '.dendro'
@@ -300,6 +313,8 @@ def plot(args):
     ax1.set_xticks([])
     ax1.set_yticks([])
 
+
+
     # subsample?
     if args.subsample:
         numpy.random.seed(args.subsample_seed)
@@ -321,7 +336,6 @@ def plot(args):
     ### make the dendrogram+matrix:
     (fig, rlabels, rmat) = sourmash_fig.plot_composite_matrix(D, labeltext,
                                              show_labels=args.labels,
-                                             show_indices=args.indices,
                                              vmin=args.vmin,
                                              vmax=args.vmax,
                                              force=args.force)

src/sourmash/fig.py

@@ -1,6 +1,6 @@
 #! /usr/bin/env python
 """
-Make plots using the distance matrix+labels output by ``sourmash compare``.
+Make plots using the distance matrix+labels output by `sourmash compare`.
 """
 from .logging import error, notify
 try:
@@ -20,11 +20,15 @@ def load_matrix_and_labels(basefile):
     return (D, labeltext)
 
 
-def plot_composite_matrix(D, labeltext, show_labels=True, show_indices=True,
+def plot_composite_matrix(D, labeltext, show_labels=True,
                           vmax=1.0, vmin=0.0, force=False):
     """Build a composite plot showing dendrogram + distance matrix/heatmap.
 
-    Returns a matplotlib figure."""
+    Returns a matplotlib figure.
+
+    If show_labels is True, display labels. Otherwise, no labels are
+    shown on the plot.
+    """
     if D.max() > 1.0 or D.min() < 0.0:
         error('This matrix doesn\'t look like a distance matrix - min value {}, max value {}', D.min(), D.max())
         if not force:
@@ -43,12 +47,8 @@ def plot_composite_matrix(D, labeltext, show_labels=True, show_indices=True,
     # plot dendrogram
     Y = sch.linkage(D, method='single')  # centroid
 
-    dendrolabels = labeltext
-    if not show_labels:
-        dendrolabels = [str(i) for i in range(len(labeltext))]
-
-    Z1 = sch.dendrogram(Y, orientation='left', labels=dendrolabels,
-                        no_labels=not show_indices, get_leaves=True)
+    Z1 = sch.dendrogram(Y, orientation='left', labels=labeltext,
+                        no_labels=not show_labels, get_leaves=True)
     ax1.set_xticks([])
 
     xstart = 0.45