TST: Update tests for HF labels

ci/create_suite.py

@@ -18,9 +18,10 @@
     BASE_MITO_PLOTLY, BASE_MITO_PLOTLY_LEGEND, BASE_MITO_PLOTLY_SPLIT,
     BASE_MITO_PLOTLY_LINEAR, BASE_MITO_PLOTLY_LINEAR_LEGEND,
     BASE_MITO_PLOTLY_LINEAR_SPLIT,
-    BASE_IMG, BASE_IMG_LABELS, BASE_IMG_LEGEND, BASE_IMG_SPLIT,
+    BASE_IMG, BASE_IMG_LABELS, BASE_IMG_LABELS_HF, BASE_IMG_LEGEND,
+    BASE_IMG_SPLIT,
     BASE_IMG_LINEAR, BASE_IMG_LINEAR_LABELS, BASE_IMG_LINEAR_LEGEND,
-    BASE_IMG_LINEAR_SPLIT,
+    BASE_IMG_LINEAR_SPLIT, BASE_IMG_LINEAR_LABELS_HF,
     BASE_IMG_PLOTLY, BASE_IMG_PLOTLY_LEGEND, BASE_IMG_PLOTLY_SPLIT,
     BASE_IMG_PLOTLY_LINEAR, BASE_IMG_PLOTLY_LINEAR_LEGEND,
     BASE_IMG_PLOTLY_LINEAR_SPLIT,
@@ -107,6 +108,8 @@ def create_sample_vcf_polar():
     plot_vcf(in_vcf=SAMPLE_VCF, save=True, output=BASE_IMG)
     plot_vcf(in_vcf=SAMPLE_VCF, save=True, output=BASE_IMG_LABELS,
              labels=True)
+    plot_vcf(in_vcf=SAMPLE_VCF, save=True, output=BASE_IMG_LABELS_HF,
+             labels=True, labels_hf=True)
     plot_vcf(in_vcf=SAMPLE_VCF, save=True, output=BASE_IMG_LEGEND,
              legend=True)
     plot_vcf(in_vcf=SAMPLE_VCF, save=True, output=BASE_IMG_SPLIT,
@@ -118,6 +121,8 @@ def create_sample_vcf_linear():
     plot_vcf(in_vcf=SAMPLE_VCF, linear=True, save=True, output=BASE_IMG_LINEAR)
     plot_vcf(in_vcf=SAMPLE_VCF, linear=True, save=True,
              output=BASE_IMG_LINEAR_LABELS, labels=True)
+    plot_vcf(in_vcf=SAMPLE_VCF, linear=True, save=True,
+             output=BASE_IMG_LINEAR_LABELS_HF, labels=True, labels_hf=True)
     plot_vcf(in_vcf=SAMPLE_VCF, linear=True, save=True,
              output=BASE_IMG_LINEAR_LEGEND, legend=True)
     plot_vcf(in_vcf=SAMPLE_VCF, linear=True, save=True,

mitoviz/cli/tests/test_mitoviz_plot.py

@@ -14,7 +14,7 @@
     SAMPLE_HF_TSV_COMM,
     BASE_IMG, BASE_IMG_LABELS, BASE_IMG_LEGEND, BASE_IMG_SPLIT,
     BASE_IMG_LINEAR, BASE_IMG_LINEAR_LABELS, BASE_IMG_LINEAR_LEGEND,
-    BASE_IMG_LINEAR_SPLIT,
+    BASE_IMG_LINEAR_SPLIT, BASE_IMG_LABELS_HF, BASE_IMG_LINEAR_LABELS_HF,
     BASE_IMG_PLOTLY, BASE_IMG_PLOTLY_LEGEND, BASE_IMG_PLOTLY_SPLIT,
     BASE_IMG_PLOTLY_LINEAR, BASE_IMG_PLOTLY_LINEAR_LEGEND,
     BASE_IMG_PLOTLY_LINEAR_SPLIT,
@@ -136,6 +136,23 @@ def test_cli_plot_polar_labels(self):
         # Cleanup
         os.remove("MITOVIZ001.png")
 
+    def test_cli_plot_polar_labels_hf(self):
+        # Given
+        base_img = cv2.imread(BASE_IMG_LABELS_HF)
+
+        # When
+        result = self.runner.invoke(cli.main,
+                                    [SAMPLE_VCF, "--labels", "--labels-hf"])
+        result_img = cv2.imread("MITOVIZ001.png")
+
+        # Then
+        self.assertEqual(0, result.exit_code)
+        self.assertTrue(os.path.isfile("MITOVIZ001.png"))
+        diff = cv2.subtract(base_img, result_img)
+        self.assertFalse(np.any(diff))
+        # Cleanup
+        os.remove("MITOVIZ001.png")
+
     def test_cli_plot_linear_labels(self):
         # Given
         base_img = cv2.imread(BASE_IMG_LINEAR_LABELS)
@@ -153,6 +170,24 @@ def test_cli_plot_linear_labels(self):
         # Cleanup
         os.remove("MITOVIZ001.png")
 
+    def test_cli_plot_linear_labels_hf(self):
+        # Given
+        base_img = cv2.imread(BASE_IMG_LINEAR_LABELS_HF)
+
+        # When
+        result = self.runner.invoke(cli.main,
+                                    [SAMPLE_VCF, "--labels", "--labels-hf",
+                                     "--linear"])
+        result_img = cv2.imread("MITOVIZ001.png")
+
+        # Then
+        self.assertEqual(0, result.exit_code)
+        self.assertTrue(os.path.isfile("MITOVIZ001.png"))
+        diff = cv2.subtract(base_img, result_img)
+        self.assertFalse(np.any(diff))
+        # Cleanup
+        os.remove("MITOVIZ001.png")
+
     def test_cli_plot_polar_legend(self):
         # Given
         base_img = cv2.imread(BASE_IMG_LEGEND)

mitoviz/plot.py

@@ -379,6 +379,7 @@ def _plot_variants_polar(sample: str,
 def _plotly_variants_polar(sample: str,
                            variants: List[_Variant],
                            labels: bool = False,
+                           labels_hf: bool = False,
                            legend: bool = False,
                            split: bool = False) -> go.Figure:
     """ Plot variants available in the given list onto a plotly polar plot.
@@ -387,6 +388,7 @@ def _plotly_variants_polar(sample: str,
         sample: sample name, used for the plot title
         variants: list of _PolarVariant instances to plot
         labels: add a label for each variant shown [default: False]
+        labels_hf: show HF value in each variant's label [default: False]
         legend: add a legend for loci colors in the plot [default: False]
         split: plot split H and L strands [default: False]
     """
@@ -449,6 +451,7 @@ def _plot_variants_linear(sample: str,
 def _plotly_variants_linear(sample: str,
                             variants: List[_Variant],
                             labels: bool = False,
+                            labels_hf: bool = False,
                             legend: bool = False,
                             split: bool = False) -> go.Figure:
     """ Plot variant available in a given list onto a plotly linear plot.
@@ -457,6 +460,7 @@ def _plotly_variants_linear(sample: str,
         sample: sample name, used for the plot title
         variants: list of _LinearVariant instances to plot
         labels: add a label for each variant shown [default: False]
+        labels_hf: show HF value in each variant's label [default: False]
         legend: add a legend for loci colors in the plot [default: False]
         split: plot split H and L strands [default: False]
     """

mitoviz/tests/constants.py

@@ -41,11 +41,13 @@
 
 BASE_IMG = os.path.join(IMGDIR, "sample.png")
 BASE_IMG_LABELS = os.path.join(IMGDIR, "sample_labels.png")
+BASE_IMG_LABELS_HF = os.path.join(IMGDIR, "sample_labels_hf.png")
 BASE_IMG_LEGEND = os.path.join(IMGDIR, "sample_legend.png")
 BASE_IMG_SPLIT = os.path.join(IMGDIR, "sample_split.png")
 
 BASE_IMG_LINEAR = os.path.join(IMGDIR, "sample_linear.png")
 BASE_IMG_LINEAR_LABELS = os.path.join(IMGDIR, "sample_linear_labels.png")
+BASE_IMG_LINEAR_LABELS_HF = os.path.join(IMGDIR, "sample_linear_labels_hf.png")
 BASE_IMG_LINEAR_LEGEND = os.path.join(IMGDIR, "sample_linear_legend.png")
 BASE_IMG_LINEAR_SPLIT = os.path.join(IMGDIR, "sample_linear_split.png")