fix bug: black when Ks values are unified

Author: zhangrengang

soi/OrthoFinder.py

@@ -932,7 +932,10 @@ def get_blast(self, sps=None):
 		if sps is None:
 			spIds = list(d_sp.values())
 		else:
-			spIds = [d_sp[sp] for sp in sps]
+			nofound = [sp for sp in sps if sp not in d_sp]
+			if nofound:
+				print('{} is not found'.format(nofound), file=sys.stderr)
+			spIds = [d_sp.get(sp) for sp in sps if sp in d_sp]
 		spIds = sorted(spIds)
 		for sp1, sp2 in itertools.product(spIds, spIds):
 			blast = '{}/Blast{}_{}.txt.gz'.format(

soi/dot_plotter.py

@@ -13,6 +13,7 @@
 
 mpl.use("Agg")
 mpl.rcParams['pdf.fonttype'] = 42
+#mpl.rcParams['image.antialiased'] = False
 
 from .RunCmdsMP import logger
 from .WGDI import AK
@@ -99,7 +100,7 @@ def dotplot_args(parser):
 						   help="basic font size of labels [default=%(default)s]")
 	group_dot.add_argument('--cfont_scale', metavar='NUM', type=float, default=0.8,
 							help="scaling factor for font size of chromosome labels [default=%(default)s]")
-	group_dot.add_argument('--dotsize', metavar='NUM', type=float, default=1, dest='point_size',
+	group_dot.add_argument('--dotsize', metavar='NUM', type=float, default=5, dest='point_size',
 						   help="dot size [default=%(default)s]")
 
 	group_orth = parser.add_argument_group('Orthology Index filter/color',
@@ -346,6 +347,7 @@ def plot_blocks(blocks, outplots, ks=None, max_ks=None, ks_hist=False, ks_cmap=N
 	ymin, ymax = 0, ylim
 	xmin, xmax = 0, xlim
 
+	
 	if ks is not None:
 		try:
 			min_ks = min([v for v in Ks if v >= 0])
@@ -361,7 +363,9 @@ def plot_blocks(blocks, outplots, ks=None, max_ks=None, ks_hist=False, ks_cmap=N
 		kXs += [None, None]  # points not plot
 		kYs += [None, None]
 		Ks += [0, max_ks]  # unify the scale
-		plt.scatter(kXs, kYs, marker=',', s=point_size, c=Ks, cmap=cmap, rasterized=True,)
+		plt.scatter(kXs, kYs, marker=',', s=point_size, c=Ks, cmap=cmap, 
+			rasterized=True, edgecolors='none',linewidths=0,
+			)
 	if same_sp:
 		plt.plot((xmin, xmax), (ymin, ymax), ls='--',
 				 color="grey", linewidth=0.8)
@@ -504,7 +508,7 @@ def plot_blocks(blocks, outplots, ks=None, max_ks=None, ks_hist=False, ks_cmap=N
 	logger.info('Output figures: {}'.format(outplots))
 	logging.disable()
 	for outplot in outplots:
-		plt.savefig(outplot, bbox_inches='tight', dpi=400) # transparent=True
+		plt.savefig(outplot, bbox_inches='tight', dpi=400, transparent=True) # transparent=True
 
 	# x/y ~ Ks
 	if plot_bin:

soi/mcscan.py

@@ -640,8 +640,8 @@ def identify_orthologous_blocks(collinearities=None, orthologs=None, fout=sys.st
 				 divide(self.retained_oi, self.post_ng)]
 		tp, fp = self.retained_oi, self.removed_oi,
 		tn, fn = self.pre_ng-self.post_ng, self.post_ng - self.retained_oi
-		recall = tp/(tp+fn)
-		precision = tp/(tp+fp)
+		recall = tp/(tp+fn) if tp+fn > 0 else None
+		precision = tp/(tp+fp) if tp+fp > 0 else None
 		line += [precision, recall]
 		print('\t'.join(map(str, line)), file=out_stats)
 	out_stats.close()

soi/ploidy_plotter.py

@@ -116,16 +116,17 @@ def plot_fold(collinearity, gff, ref, qry, **kargs):
 							**kargs)
 		data += [np.array(sorted(d_fold.items()))]
 		#print(sp, sorted(d_fold.items()))
-	return plot_bars(data, **kargs)
+	return plot_bars(data, ref=ref, **kargs)
 
 
 def plot_bars(data, titles, ax=None, outfigs=None, nrow=1, ncol=1, fontsize=10, 
 			  suptitle=None, max_ploidy=10, color='white', edgecolor='black',
 			  ylabel='Number of windows', xlabel='Synteny depth', 
-			  output_depth=None, mode='w', 
+			  output_depth=None, mode='w', ref=None,
 			  **kargs):
 	if output_depth:
-		save_depth_table(data, titles, output_depth=output_depth, mode=mode, max_ploidy=max_ploidy)
+		save_depth_table(data, titles, output_depth=output_depth, 
+			mode=mode, max_ploidy=max_ploidy, ref=ref)
 	if ax is None:
 		if nrow*ncol == 1:
 			ax = plt.subplot(111)
@@ -161,12 +162,12 @@ def plot_bars(data, titles, ax=None, outfigs=None, nrow=1, ncol=1, fontsize=10,
 			plt.savefig(outfig)
 	else:
 		return ax
-def save_depth_table(data, titles, output_depth=None, mode='w', max_ploidy=10):
+def save_depth_table(data, titles, ref=None, output_depth=None, mode='w', max_ploidy=10):
     """
     每行一个物种，列为不同深度 (1 to max_ploidy)
     """
     # 1. 构建表头: Species, 1, 2, 3, ..., 10+
-    header = ["Species"] + [str(i) for i in range(1, max_ploidy)] + [f"{max_ploidy}+"]
+    header = ['Reference', "Query"] + [str(i) for i in range(1, max_ploidy)] + [f"{max_ploidy}+"]
 
     rows = [header]
 
@@ -183,14 +184,14 @@ def save_depth_table(data, titles, output_depth=None, mode='w', max_ploidy=10):
                 counts[depth] += count
 
         # 构造当前行：物种名 + 各深度的计数
-        row = [species] + [str(counts[p]) for p in range(1, max_ploidy + 1)]
+        row = [str(ref), species] + [str(counts[p]) for p in range(1, max_ploidy + 1)]
         rows.append(row)
 
     # 3. 拼接为 TSV 文本
     output_text = "\n".join(["\t".join(row) for row in rows]) + "\n"
 
     # 4. 输出
-    if output_depth:
+    if output_depth and output_depth != 'stdout':
         with open(output_depth, mode=mode, encoding='utf-8') as f:
             f.write(output_text)
     else: