Update example figures.

examples/pr_fig_a.py

@@ -1,5 +1,6 @@
 import pyranges as pr
 import pyranges_plot as prp
+from pyranges_plot.plot_features import builtin_themes
 
 # Load data
 g = pr.PyRanges(
@@ -40,6 +41,10 @@
 )
 
 # Get plot
+prp.set_engine("plt")
+cmap = builtin_themes["Mariotti_lab"]["colormap"]
+cmap += ["lightpink", "lightyellow"]
+prp.set_options("colormap", cmap)
 prp.plot(
     [
         g,
@@ -48,10 +53,12 @@
         pr.concat([g_subseq, g_subseq_id]),
         pr.concat([g_spl_subseq_for, g_spl_subseq_rev]),
     ],
-    engine="plt",
+    warnings=False,
     id_col="transcript_id",
     title_chr=" ",
-    limits=(-12, None),
-    to_file="fig3_1.png",
-    file_size=(7, 5),
+    limits=(-15, None),
+    to_file=("fig3_1.png", (700, 500)),
+    text=True,
+    text_pad=0.05,
+    theme="Mariotti_lab",
 )

examples/pr_fig_b.py

@@ -26,13 +26,16 @@
 r_tile["transcript_id"] = ["r.tile(2)"] * len(r_tile)  # rename for plot
 
 # Get plot
+prp.set_engine("plt")
+
 prp.plot(
     [r, r_window, tile_g, r_tile],
-    engine="plt",
     id_col="transcript_id",
     exon_border="black",
     title_chr=" ",
-    limits=(-6, None),
-    to_file="fig3_2.png",
-    file_size=(7, 4),
+    limits=(-8, None),
+    to_file=("fig3_2.png", (700, 400)),
+    text=True,
+    text_pad=0.05,
+    theme="Mariotti_lab",
 )

examples/pr_fig_c.py

@@ -1,5 +1,6 @@
 import pyranges as pr
 import pyranges_plot as prp
+import matplotlib.pyplot as plt
 
 # Load data
 a = pr.PyRanges(
@@ -8,6 +9,7 @@
         "Start": [2, 12, 17, 22, 27, 32, 33],
         "End": [5, 14, 20, 26, 29, 37, 36],
         "Strand": ["+"] * 2 + ["-"] * 3 + ["+"] * 2,
+        "color_by": ["a"] * 7,
     }
 )
 
@@ -17,6 +19,7 @@
         "Start": [6, 11, 18, 24, 34],
         "End": [8, 13, 19, 28, 36],
         "Strand": ["+"] * 3 + ["-"] * 1 + ["+"] * 1,
+        "color_by": ["b"] * 5,
     }
 )
 
@@ -25,15 +28,23 @@
 a_ov_b_slack = a.overlap(b, slack=2)
 a_ov_b_nostrand = a.overlap(b, strand_behavior="ignore")
 a_ov_b_opstrand = a.overlap(b, strand_behavior="opposite")
+for pr_obj in [a_ov_b, a_ov_b_slack, a_ov_b_nostrand, a_ov_b_opstrand]:
+    pr_obj["color_by"] = ["overlap"] * len(pr_obj)
 
 # intersection
 a_inters_b = a.intersect(b)
+a_inters_b["color_by"] = ["intersect"] * len(a_inters_b)
 a_setinters_b = a.set_intersect(b)
+a_setinters_b["color_by"] = ["setintersect"] * len(a_setinters_b)
+
 
 # subtract
-a_subt_b = a.subtract_ranges(b)  ## is this a.subtract(the slack one)
+a_subt_b = a.subtract_ranges(b)
+a_subt_b["color_by"] = ["subtract"] * len(a_subt_b)
 
 # Get plot
+prp.set_engine("plt")
+plt.rcParams["figure.subplot.left"] = 0.4  # Adjust the left margin
 prp.plot(
     [
         a,
@@ -46,13 +57,23 @@
         a_setinters_b,
         a_subt_b,
     ],
-    engine="plt",
+    y_labels=[
+        "a",
+        "b",
+        "a.overlap(b)",
+        "a.overlap(b, slack=2)",
+        "a.overlap(b, strand_behavior='ignore')",
+        "a.overlap(b, strand_behavior='opposite')",
+        "a.intersect(b)",
+        "a.set_intersect(b)",
+        "a.subtract_ranges(b)",
+    ],
     title_chr=" ",
-    text=False,
-    to_file="fig3_3.png",
-    file_size=(5, 4),
-    colormap=["#4169E1"],
+    warnings=False,
+    to_file=("fig3_3.png", (800, 400)),
+    color_col="color_by",
     arrow_color="black",
-    arrow_line_width=0.6,
-    arrow_size_min=0.001,
+    arrow_line_width=0.5,
+    arrow_size=0.0005,
+    theme="Mariotti_lab",
 )