From 024fb4a4d64fd04d75e002f7c2c761e95518f863 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sat, 3 Aug 2024 16:32:44 -0400
Subject: [PATCH] add setable alpha level to add_shades

---
 specparam/plts/utils.py            | 15 +++++++++++----
 specparam/tests/plts/test_utils.py |  4 ++++
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/specparam/plts/utils.py b/specparam/plts/utils.py
index f9156282..70fd1372 100644
--- a/specparam/plts/utils.py
+++ b/specparam/plts/utils.py
@@ -65,7 +65,8 @@ def set_alpha(n_points):
     return alpha
 
 
-def add_shades(ax, shades, colors='r', add_center=False, logged=False):
+def add_shades(ax, shades, colors='r', alpha=0.2,
+               add_center=False, center_alpha=0.6, logged=False):
     """Add shaded regions to a plot.
 
     Parameters
@@ -76,8 +77,13 @@ def add_shades(ax, shades, colors='r', add_center=False, logged=False):
         Shaded region(s) to add to plot, defined as [lower_bound, upper_bound].
     colors : str or list of string
         Color(s) to plot shades.
+    alpha : float or list of float, optional, default: 0.2
+        The alpha level to add the shade regions with.
+        If a list, can specify a separate alpha level per shade.
     add_center : boolean, default: False
         Whether to add a line at the center point of the shaded regions.
+    center_alpha : float, optional, default: 0.6
+        The alpha level for the center line, if added.
     logged : boolean, default: False
         Whether the shade values should be logged before applying to plot axes.
     """
@@ -87,16 +93,17 @@ def add_shades(ax, shades, colors='r', add_center=False, logged=False):
         shades = [shades]
 
     colors = repeat(colors) if not isinstance(colors, list) else colors
+    alphas = repeat(alpha) if not isinstance(alpha, list) else alpha
 
-    for shade, color in zip(shades, colors):
+    for shade, color, alpha in zip(shades, colors, alphas):
 
         shade = np.log10(shade) if logged else shade
 
-        ax.axvspan(shade[0], shade[1], color=color, alpha=0.2, lw=0)
+        ax.axvspan(shade[0], shade[1], color=color, alpha=alpha, lw=0)
 
         if add_center:
             center = sum(shade) / 2
-            ax.axvspan(center, center, color='k', alpha=0.6)
+            ax.axvspan(center, center, color='k', alpha=center_alpha)
 
 
 def recursive_plot(data, plot_function, ax, **kwargs):
diff --git a/specparam/tests/plts/test_utils.py b/specparam/tests/plts/test_utils.py
index edfe80d1..a88accfa 100644
--- a/specparam/tests/plts/test_utils.py
+++ b/specparam/tests/plts/test_utils.py
@@ -33,6 +33,10 @@ def test_add_shades(skip_if_no_mpl):
 
     add_shades(check_ax(None), [4, 8])
 
+@plot_test
+def test_add_shades_multi(skip_if_no_mpl):
+    add_shades(check_ax(None), [[4, 8], [8, 12], [12, 25]], colors=['b', 'c', 'y'], alpha=0.3)
+
 @plot_test
 def test_recursive_plot(skip_if_no_mpl):