Update manuscript figures.

examples/pr_figs_results.py → examples/pr_fig_2.py

@@ -48,15 +48,15 @@
     id_col="Parent",
     thick_cds=True,
     text=False,
-    to_file="fig2_1.png",
-    file_size=(5, 3),
+    to_file=("fig_2a.png", (500, 300)),
+    arrow_size=0.04,
 )
 
 # show introns off and save png (Figure 2.2)
 prp.plot(
     gr_1,
     id_col="transcript_id",
     shrink=True,
-    to_file="fig2_2.png",
-    file_size=(5, 3),
+    to_file=("fig_2b.png", (500, 300)),
+    arrow_size=0.04,
 )

examples/pr_fig_a.py → examples/pr_fig_3a.py

@@ -44,7 +44,7 @@
 prp.set_engine("plt")
 cmap = builtin_themes["Mariotti_lab"]["colormap"]
 cmap += ["lightpink", "lightyellow"]
-prp.set_options("colormap", cmap)
+
 prp.plot(
     [
         g,
@@ -57,8 +57,9 @@
     id_col="transcript_id",
     title_chr=" ",
     limits=(-15, None),
-    to_file=("fig3_1.png", (700, 500)),
+    to_file=("fig_3a.png", (700, 500)),
     text=True,
     text_pad=0.05,
     theme="Mariotti_lab",
+    colormap=cmap,
 )

examples/pr_fig_b.py → examples/pr_fig_3b.py

@@ -34,7 +34,7 @@
     exon_border="black",
     title_chr=" ",
     limits=(-8, None),
-    to_file=("fig3_2.png", (700, 400)),
+    to_file=("fig_3b.png", (700, 400)),
     text=True,
     text_pad=0.05,
     theme="Mariotti_lab",

examples/pr_fig_c.py → examples/pr_fig_3c.py

@@ -45,6 +45,8 @@
 
 # Get plot
 prp.set_engine("plt")
+# customize left margin to fit titles
+ori_margin = plt.rcParams["figure.subplot.left"]
 plt.rcParams["figure.subplot.left"] = 0.4  # Adjust the left margin
 prp.plot(
     [
@@ -71,10 +73,12 @@
     ],
     title_chr=" ",
     warnings=False,
-    to_file=("fig3_3.png", (800, 400)),
+    to_file=("fig_3c.png", (800, 400)),
     color_col="to_color",
     arrow_color="black",
     arrow_line_width=0.5,
-    # arrow_size=3,
     theme="Mariotti_lab",
 )
+
+# reset rcparams
+plt.rcParams["figure.subplot.left"] = ori_margin

src/pyranges_plot/matplotlib_base/data2plot.py

@@ -36,7 +36,7 @@ def plot_direction(
 
     if strand:
         # create and plot direction lines
-        if item_size > item_threshold:
+        if item_size <= item_threshold:
             dir_flag = 1
             ##diagonal_line = OX arrow extension(item middle point +- incl), OY arrow extension (item middle point + half of exon width)
             top_plus = (
@@ -242,7 +242,7 @@ def plot_row(
         plot_direction(
             ax,
             strand,
-            incl,
+            incl * 2,
             stop - start,  # itself as threshold
             start,
             stop,
@@ -367,8 +367,8 @@ def apply_plot_intron(row):
             plot_direction(
                 ax,
                 strand,
-                intron_size,
                 arrow_size,
+                intron_size,
                 start,
                 stop,
                 incl,

src/pyranges_plot/plotly_base/data2plot.py

@@ -38,7 +38,7 @@ def plot_direction(
 
     if strand:
         # create and plot direction lines
-        if item_size > item_threshold:
+        if item_size <= item_threshold:
             dir_flag = 1
             ##diagonal_line = OX arrow extension(item middle point +- incl), OY arrow extension (item middle point + half of exon width)
             top_plus = (
@@ -262,7 +262,7 @@ def plot_row(
             fig,
             strand,
             genename,
-            incl,
+            incl * 2,
             stop - start,  # itself as threshold
             start,
             stop,
@@ -393,8 +393,8 @@ def apply_plot_intron(row):
                 fig,
                 strand,
                 genename,
-                intron_size,
                 arrow_size,  # size of arrow as threshold
+                intron_size,
                 start,
                 stop,
                 incl,