Merge pull request #90 from BranniganLab/22-get_cmap-is-deprecated-in…

…-matplotlib

22 get cmap is deprecated in matplotlib

python/plotting.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Nov 11 14:41:24 2024.
+
+@author: js2746
+"""
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib.colors import ListedColormap
+
+
+def make_custom_colormap():
+    """
+    Make a custom colormap for plotting. The colormap starts at 0.35 to ensure \
+    that there is a visual difference between 0 (no signal) and depleted (near-\
+    zero enrichment).
+
+    Returns
+    -------
+    my_cmap : matplotlib colormap
+        The colormap to use when plotting.
+
+    """
+    depleted = plt.colormaps['RdGy_r']
+    enriched = plt.colormaps['bwr']
+    newcolors = np.concatenate([depleted(np.linspace(0.35, 0.5, 128)), enriched(np.linspace(0.5, 1, 128))])
+    my_cmap = ListedColormap(newcolors)
+    return my_cmap

python/preliminaries.ipynb

@@ -16,23 +16,11 @@
     "from DTA.enrichment_plotters import polar_plot, get_file_list, get_helices, read_rep\n",
     "from DTA.polarDensity_helper import Coord_Get, get_header_info\n",
     "from DTA.site_distributions import outline_site, make_symmetric_sites, combine_sites, plot_density, Site\n",
+    "from plotting import make_custom_colormap\n",
+    "my_cmap = make_custom_colormap()\n",
     "plt.rcParams['axes.grid'] = False "
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Enrichment plot colormap\n",
-    "from matplotlib.colors import ListedColormap\n",
-    "depleted = plt.cm.get_cmap('RdGy_r', 256)\n",
-    "enriched = plt.cm.get_cmap('bwr', 256)\n",
-    "newcolors = np.concatenate([depleted(np.linspace(0.35, 0.5, 128)), enriched(np.linspace(0.5,1,128))])\n",
-    "my_cmap = ListedColormap(newcolors)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -382,7 +370,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "jupEnv",
+   "display_name": "base",
    "language": "python",
    "name": "python3"
   },
@@ -396,7 +384,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,