fix bug and update readme

README.md

@@ -134,6 +134,10 @@ Input custom feature (e.g. transposable element, gene) sequences for subgenome-s
 ```
 subphaser -i genome.fasta.gz -c sg.config -custom_features TEs.fasta genes.fasta
 ```
+Define custom colors for subgenomes:
+```
+subphaser -i genome.fasta.gz -c sg.config -colors "#f9c00c,#00b9f1,#7200da"
+```
 ### Run SubPhaser through Singularity/Apptainer ###
 Alternatively, you can run `subphaser` through Singularity/Apptainer container:
 ```

subphaser/Cluster.py

@@ -45,7 +45,7 @@ def __init__(self, datafile, n_clusters, sg_prefix='SG', sg_color=None,
 			self.d_sg = self.assign_subgenomes()
 		if bootstrap:
 			self.d_bs = self.bootstrap(replicates, jackknife)
-	def pca(self, outfig, n_components=2, ):
+	def pca(self, outfig, n_components=2, sg_color=None):
 		pca = PCA(n_components=n_components)
 		X_pca = pca.fit_transform(self.data)
 		percent = pca.explained_variance_ratio_ * 100

subphaser/__main__.py

@@ -67,8 +67,8 @@ def makeArgparse():
 					help="Output directory [default=%(default)s]")
 	group_out.add_argument('-tmpdir', default='tmp', type=str, metavar='DIR',
 					help="Temporary directory [default=%(default)s]")
-	group_out.add_argument('-colors', default=None, dest='colors', metavar='HEX,HEX...',
-                    help="Subgenome colors [default=%(default)s]")
+	group_out.add_argument('-colors', default=None, dest='colors', metavar='HEX,HEX[,...]',
+                    help="Subgenome colors in hex codes [default=%(default)s]")
 
 	# kmer
 	group_kmer = parser.add_argument_group('Kmer', 'Options to count and filter kmers')

subphaser/colors.py

@@ -23,7 +23,9 @@ def colors_rgb(self):
 		return [','.join(map(str, v.bitmap_rgb())) for v in colors_lst]
 	@property 
 	def colors_r(self):
-		return 'c({})'.format(','.join(map(repr, self.olors_hex)))
+		return 'c({})'.format(','.join(map(repr, self.colors_hex)))
+	def __str__(self):
+		return str(self.colors_hex)
 
 class Colors:
 	def __init__(self, n):