diversity complete

jcvi/graphics/base.py

@@ -4,6 +4,7 @@
 import copy
 import os.path as op
 from os import remove
+
 import sys
 import logging
 
@@ -12,6 +13,7 @@
 logging.getLogger("PIL").setLevel(logging.INFO)
 
 from functools import partial
+from typing import Optional, List, Tuple, Union
 
 import numpy as np
 import matplotlib as mpl
@@ -35,7 +37,6 @@
     FancyArrowPatch,
     FancyBboxPatch,
 )
-from typing import Optional, List, Tuple, Union
 
 from ..apps.base import datadir, glob, listify, logger, sample_N, which
 from ..formats.base import LineFile
@@ -275,14 +276,20 @@ def prettyplot():
 
 
 def normalize_axes(axes):
+    """
+    Normalize the axes to have the same scale.
+    """
     axes = listify(axes)
     for ax in axes:
         ax.set_xlim(0, 1)
         ax.set_ylim(0, 1)
         ax.set_axis_off()
 
 
-def panel_labels(ax, labels, size=16):
+def panel_labels(ax, labels, size: int = 16):
+    """
+    Add panel labels (A, B, ...) to a figure.
+    """
     for xx, yy, panel_label in labels:
         if rcParams["text.usetex"]:
             panel_label = r"$\textbf{{{0}}}$".format(panel_label)

jcvi/graphics/landscape.py

@@ -352,11 +352,11 @@ def draw_depth(
             alpha=0.5,
         )
 
-    # vertical lines for all the breaks
+    # Vertical lines for all the breaks
     for pos in starts.values():
         ax.plot((pos, pos), (0, maxdepth), "-", lw=1, color=sepcolor)
 
-    # beautify the numeric axis
+    # Beautify the numeric axis
     for tick in ax.get_xticklines() + ax.get_yticklines():
         tick.set_visible(False)
 
@@ -444,7 +444,7 @@ def draw_multi_depth(
         bed = Bed(bedfile)
 
         if ypos > 0.001:
-            root.plot((0, 1), (ypos, ypos), "-", lw=2, color="lightslategray")
+            root.plot((0.02, 0.98), (ypos, ypos), "-", lw=2, color="lightslategray")
 
         title = titleinfo.get(bedfile, pf.split("_", 1)[0])
         subtitle = None

jcvi/projects/jcvi.py

@@ -7,10 +7,13 @@
 
 import sys
 
+import networkx as nx
+
 from ..apps.base import ActionDispatcher, OptionParser, logger
 from ..assembly.geneticmap import draw_geneticmap_heatmap
 from ..assembly.hic import draw_hic_heatmap
 from ..assembly.kmer import draw_ks_histogram
+from ..compara.pedigree import Pedigree, calculate_inbreeding
 from ..graphics.base import normalize_axes, panel_labels, plt, savefig
 from ..graphics.landscape import draw_multi_depth
 
@@ -111,6 +114,23 @@ def diversity(args):
 
     # Panel A
     logger.info("Plotting pedigree")
+    ped = Pedigree(pedfile)
+    pngfile = f"{pedfile}.png"
+    inb = calculate_inbreeding(ped, ploidy=4, N=10000)
+
+    G = ped.to_graph(inb, title="Pedigree of Variety1")
+    A = nx.nx_agraph.to_agraph(G)
+    dpi = 300
+    A.draw(pngfile, prog="dot", args=f"-Gdpi={dpi}")
+    logger.info("Pedigree graph written to `%s`", pngfile)
+
+    M = plt.imread(pngfile)
+    width, height = M.shape[1] / dpi, M.shape[0] / dpi
+    logger.info("Image size: %.2f x %.2f (dpi=%d)", width, height, dpi)
+
+    # Force aspect ratio to be equal
+    ax1_root.imshow(M)
+    ax1_root.set_axis_off()
 
     # Panel B
     logger.info("Plotting depth distribution across genomes")
@@ -119,7 +139,7 @@ def diversity(args):
     ypos = 1 - yinterval
     panel_roots, panel_axes = [], []
     for _ in range(npanels):
-        panel_root = root if npanels == 1 else fig.add_axes((0.25, ypos, 1, yinterval))
+        panel_root = fig.add_axes((0.25, ypos, 0.75, yinterval))
         panel_ax = fig.add_axes(
             (0.25 + 0.1 * 0.75, ypos + 0.2 * yinterval, 0.8 * 0.75, 0.65 * yinterval)
         )
@@ -139,11 +159,11 @@ def diversity(args):
     )
 
     labels = (
-        (0.25 * 0.1, 0.95, "A"),
+        (0.02, 0.95, "A"),
         (0.25 + 0.25 * 0.1, 0.95, "B"),
     )
     panel_labels(root, labels)
-    normalize_axes([root, ax1_root, ax2_root])
+    normalize_axes([root, ax2_root])
 
     image_name = "diversity.pdf"
     savefig(image_name, dpi=iopts.dpi, iopts=iopts)

jcvi/projects/misc.py

@@ -75,7 +75,7 @@ def waterlilyGOM(args):
     pf = datafile.rsplit(".", 1)[0]
 
     fig = plt.figure(1, (iopts.w, iopts.h))
-    root = fig.add_axes([0, 0, 1, 1])
+    root = fig.add_axes((0, 0, 1, 1))
 
     margin, rmargin = 0.15, 0.19  # Left and right margin
     leafinfo = LeafInfoFile("leafinfo.csv").cache