Updated color palette for more discernible colors

assets/paper/jupyter/Figure-4-haplotypes-p_arm.ipynb

@@ -340,10 +340,9 @@
    "source": [
     "IMSHOW_PALETTE = {\n",
     "    None: [.7, .7, .7],\n",
-    "    \"CCCTAA\": [.1, .5, .2],\n",
+    "    \"CCCTAA\": [.0, .4, .1],\n",
     "    \"CCCTCA\": [1, 1, 0],\n",
-    "    \"CCCCTAA\": [.8, .4, .6],\n",
-    "    \"CCTAA\": [.5, .9, 1],\n",
+    "    \"CCCCTAA\": [.5, .9, 1],\n",
     "}\n",
     "\n",
     "def plot_densities(densities, chrom, data2d, ecx, gf, extent, bin_size=100):\n",
@@ -355,7 +354,7 @@
     "            ps = np.pad(ps, ((0, 0), (MAXLEN-ps.shape[1], 0)))\n",
     "        elif ps.shape[1] > MAXLEN:\n",
     "            ps = ps[:,-MAXLEN:]\n",
-    "        pa = section_to_RGB(np.clip(uniform_filter1d(ps[:,::-1], 5, 1)[:,::-1], a_min=0.0, a_max=1.0), color, 1.5)\n",
+    "        pa = section_to_RGB(np.clip(uniform_filter1d(ps[:,::-1], 5, 1)[:,::-1], a_min=0.0, a_max=1.0), color, 2)\n",
     "        ax.imshow(pa, extent=extent, interpolation=\"nearest\")\n",
     "    ticklabels=(-np.linspace(MAXLEN//100, 0, MAXLEN//100+1).astype(int)).astype(str)\n",
     "    fullaxislen = len(ticklabels)\n",
@@ -678,18 +677,12 @@
     "\n",
     "axs[0].add_patch(Rectangle((0,3), 1.5, .65, facecolor=\"#119933\", edgecolor=\"black\"))\n",
     "axs[0].text(x=1.75, y=3.25, s=\"CCCTAA\", fontsize=15, va=\"center\")\n",
-    "axs[0].add_patch(Rectangle((0,2), 1.5, .65, facecolor=\"#AA6699\", edgecolor=\"black\"))\n",
+    "axs[0].add_patch(Rectangle((0,2), 1.5, .65, facecolor=\"#88DFEF\", edgecolor=\"black\"))\n",
     "axs[0].text(x=1.75, y=2.25, s=\"CCCCTAA\", fontsize=15, va=\"center\")\n",
-    "if INCLUDE_FIVEMER:\n",
-    "    axs[0].add_patch(Rectangle((0,1), 1.5, .65, facecolor=\"#88CCEE\", edgecolor=\"black\"))\n",
-    "    axs[0].text(x=1.75, y=1.25, s=\"CCTAA\", fontsize=15, va=\"center\")\n",
-    "    axs[0].add_patch(Rectangle((0,0), 1.5, .65, facecolor=\"#DDDDDD\", edgecolor=\"black\"))\n",
-    "    axs[0].text(x=1.75, y=0.25, s=\"background\", fontsize=13, va=\"center\")\n",
-    "else:\n",
-    "    axs[0].add_patch(Rectangle((0,1), 1.5, .65, facecolor=\"#DDDDDD\", edgecolor=\"black\"))\n",
-    "    axs[0].text(x=1.75, y=1.25, s=\"background\", fontsize=13, va=\"center\")\n",
-    "    axs[0].set(frame_on=False)\n",
-    "    axs[0].add_patch(Rectangle((-.4, .6), 5.3, 3.45, facecolor=\"none\", edgecolor=\"black\", lw=1, clip_on=False))\n",
+    "axs[0].add_patch(Rectangle((0,1), 1.5, .65, facecolor=\"#DDDDDD\", edgecolor=\"black\"))\n",
+    "axs[0].text(x=1.75, y=1.25, s=\"background\", fontsize=13, va=\"center\")\n",
+    "axs[0].set(frame_on=False)\n",
+    "axs[0].add_patch(Rectangle((-.4, .6), 5.3, 3.45, facecolor=\"none\", edgecolor=\"black\", lw=1, clip_on=False))\n",
     "axs[0].set(xticks=[], yticks=[], xlim=(-.4, 4.8), ylim=(-0.7, 4.4))\n",
     "axs[0].set_title(\"Motif densities\", fontsize=17)\n",
     "\n",

assets/paper/jupyter/Figure-5-haplotypes-q_arm.ipynb

@@ -337,10 +337,9 @@
    "source": [
     "IMSHOW_PALETTE = {\n",
     "    None: [.7, .7, .7],\n",
-    "    \"TTAGGG\": [.1, .5, .2],\n",
+    "    \"TTAGGG\": [.0, .4, .1],\n",
     "    \"TGAGGG\": [1, 1, 0],\n",
-    "    \"TTAGGGG\": [.8, .4, .6],\n",
-    "    \"TTAGG\": [.5, .9, 1],\n",
+    "    \"TTAGGGG\": [.5, .9, 1],\n",
     "}\n",
     "\n",
     "def plot_densities(densities, chrom, data2d, ecx, gf, extent, bin_size=100):\n",
@@ -673,7 +672,7 @@
     "axs[2].text(x=1.75, y=3.25, s=\"TTAGGG\", fontsize=15, va=\"center\")\n",
     "axs[2].add_patch(Rectangle((0,2), 1.5, .65, facecolor=\"#EEDD77\", edgecolor=\"black\"))\n",
     "axs[2].text(x=1.75, y=2.25, s=\"TGAGGG\", fontsize=15, va=\"center\")\n",
-    "axs[2].add_patch(Rectangle((0,1), 1.5, .65, facecolor=\"#AA6699\", edgecolor=\"black\"))\n",
+    "axs[2].add_patch(Rectangle((0,1), 1.5, .65, facecolor=\"#88DFEF\", edgecolor=\"black\"))\n",
     "axs[2].text(x=1.75, y=1.25, s=\"TTAGGGG\", fontsize=15, va=\"center\")\n",
     "axs[2].add_patch(Rectangle((0,0), 1.5, .65, facecolor=\"#DDDDDD\", edgecolor=\"black\"))\n",
     "axs[2].text(x=1.75, y=0.25, s=\"background\", fontsize=13, va=\"center\")\n",

assets/paper/jupyter/Figure-S4-haplotypes-constrained-p_arm.ipynb

@@ -323,10 +323,9 @@
    "source": [
     "IMSHOW_PALETTE = {\n",
     "    None: [.7, .7, .7],\n",
-    "    \"CCCTAA\": [.1, .5, .2],\n",
+    "    \"CCCTAA\": [.0, .4, .1],\n",
     "    \"CCCTCA\": [1, 1, 0],\n",
-    "    \"CCCCTAA\": [.8, .4, .6],\n",
-    "    \"CCTAA\": [.5, .9, 1],\n",
+    "    \"CCCCTAA\": [.5, .9, 1],\n",
     "}\n",
     "\n",
     "def plot_densities(densities, chrom, data2d, ecx, gf, extent, bin_size=100):\n",
@@ -338,7 +337,7 @@
     "            ps = np.pad(ps, ((0, 0), (MAXLEN-ps.shape[1], 0)))\n",
     "        elif ps.shape[1] > MAXLEN:\n",
     "            ps = ps[:,-MAXLEN:]\n",
-    "        pa = section_to_RGB(np.clip(uniform_filter1d(ps[:,::-1], 5, 1)[:,::-1], a_min=0.0, a_max=1.0), color, 1.5)\n",
+    "        pa = section_to_RGB(np.clip(uniform_filter1d(ps[:,::-1], 5, 1)[:,::-1], a_min=0.0, a_max=1.0), color, 2)\n",
     "        ax.imshow(pa, extent=extent, interpolation=\"nearest\")\n",
     "    ticklabels=(-np.linspace(MAXLEN//100, 0, MAXLEN//100+1).astype(int)).astype(str)\n",
     "    fullaxislen = len(ticklabels)\n",

assets/paper/jupyter/Figure-S5-haplotypes-constrained-q_arm.ipynb

@@ -320,10 +320,9 @@
    "source": [
     "IMSHOW_PALETTE = {\n",
     "    None: [.7, .7, .7],\n",
-    "    \"TTAGGG\": [.1, .5, .2],\n",
+    "    \"TTAGGG\": [.0, .4, .1],\n",
     "    \"TGAGGG\": [1, 1, 0],\n",
-    "    \"TTAGGGG\": [.8, .4, .6],\n",
-    "    \"TTAGG\": [.5, .9, 1],\n",
+    "    \"TTAGGGG\": [.5, .9, 1],\n",
     "}\n",
     "\n",
     "def plot_densities(densities, chrom, data2d, ecx, gf, extent, subject, bin_size=100):\n",
@@ -336,7 +335,7 @@
     "            ps = np.pad(ps, ((0, 0), (0, MAXLEN-ps.shape[1])))\n",
     "        elif ps.shape[1] > MAXLEN:\n",
     "            ps = ps[:,:MAXLEN]\n",
-    "        pa = section_to_RGB(np.clip(uniform_filter1d(ps, 5, 1), a_min=0.0, a_max=1.0), color, 1.5)\n",
+    "        pa = section_to_RGB(np.clip(uniform_filter1d(ps, 5, 1), a_min=0.0, a_max=1.0), color, 2)\n",
     "        ax.imshow(pa, extent=extent, interpolation=\"nearest\")\n",
     "    ticklabels=np.linspace(0, MAXLEN//100, MAXLEN//100+1).astype(int).astype(str)\n",
     "    fullaxislen = len(ticklabels)\n",

edgecaselib/formats.py

@@ -25,8 +25,8 @@
 TOL_COLORSCHEME = OrderedDict([
     ("green",   "#117733"),
     ("yellow",  "#DDCC77"),
+    ("cyan",    "#88DDFF"),
     ("magenta", "#AA4499"),
-    ("cyan",    "#88CCEE"),
     ("blue",    "#332288"),
     ("red",     "#882255"),
     ("teal",    "#44AA99"),
@@ -39,8 +39,8 @@
 PAPER_PALETTE = OrderedDict([
     ("TTAGGG", TOL_COLORSCHEME["green"]),
     ("TGAGGG", TOL_COLORSCHEME["yellow"]),
-    ("TTAGGGG", TOL_COLORSCHEME["magenta"]),
-    ("TTAGG", TOL_COLORSCHEME["cyan"]),
+    ("TTAGGGG", TOL_COLORSCHEME["cyan"]),
+    ("TTAGG", TOL_COLORSCHEME["magenta"]),
     ("TTAGGGTTAGGGG", TOL_COLORSCHEME["blue"]),
     ("TTGGGG", TOL_COLORSCHEME["red"]),
     ("TCAGGG", TOL_COLORSCHEME["teal"]),
@@ -50,8 +50,8 @@
 PAPER_PALETTE_RC = OrderedDict([
     ("CCCTAA", TOL_COLORSCHEME["green"]),
     ("CCCTCA", TOL_COLORSCHEME["yellow"]),
-    ("CCCCTAA", TOL_COLORSCHEME["magenta"]),
-    ("CCTAA", TOL_COLORSCHEME["cyan"]),
+    ("CCCCTAA", TOL_COLORSCHEME["cyan"]),
+    ("CCTAA", TOL_COLORSCHEME["magenta"]),
     ("CCCCTAACCCTAA", TOL_COLORSCHEME["blue"]),
     ("CCCCAA", TOL_COLORSCHEME["red"]),
     ("CCCTGA", TOL_COLORSCHEME["teal"]),