dev sync

jcvi/assembly/geneticmap.py

@@ -23,6 +23,7 @@
 from ..graphics.base import (
     Rectangle,
     draw_cmap,
+    normalize_axes,
     plt,
     plot_heatmap,
     savefig,
@@ -384,14 +385,14 @@ def draw_geneticmap_heatmap(root, ax, mstmap: str, subsample: int):
     M, markerbedfile, nmarkers = read_subsampled_matrix(mstmap, subsample)
 
     # Plot chromosomes breaks
-    bed = Bed(markerbedfile)
-    xsize = len(bed)
+    b = Bed(markerbedfile)
+    xsize = len(b)
     extent = (0, nmarkers)
     chr_labels = []
     ignore_size = 20
 
     breaks = []
-    for seqid, beg, end in bed.get_breaks():
+    for seqid, beg, end in b.get_breaks():
         ignore = abs(end - beg) < ignore_size
         pos = (beg + end) / 2
         chr_labels.append((seqid, pos, ignore))
@@ -422,9 +423,7 @@ def draw_geneticmap_heatmap(root, ax, mstmap: str, subsample: int):
     m = mstmap.split(".")[0]
     root.text(0.5, 0.06, f"Linkage Disequilibrium between {m} markers", ha="center")
 
-    root.set_xlim(0, 1)
-    root.set_ylim(0, 1)
-    root.set_axis_off()
+    normalize_axes(root)
 
 
 def heatmap(args):

jcvi/projects/jcvi.py

@@ -5,7 +5,10 @@
 Functions in this script produce figures in the JCVI manuscript.
 """
 
+import sys
+
 from ..apps.base import ActionDispatcher, OptionParser, logger
+from ..assembly.geneticmap import draw_geneticmap_heatmap
 from ..graphics.base import normalize_axes, panel_labels, plt, savefig
 
 
@@ -19,31 +22,35 @@ def genomebuild(args):
     C. Hi-C contact map concordance
     """
     p = OptionParser(genomebuild.__doc__)
-    _, args, iopts = p.set_image_options(args, figsize="15x5")
+    _, args, iopts = p.set_image_options(args, figsize="21x7")
 
     if len(args) != 4:
         sys.exit(not p.print_help())
 
-    reads_histo, geneticmap_matrix, hic_matrix, hic_json = args
+    reads_histo, mstmap, hic_matrix, hic_json = args
 
     fig = plt.figure(1, (iopts.w, iopts.h))
     root = fig.add_axes((0, 0, 1, 1))
-    ax1 = fig.add_axes((0.1, 0.1, 0.32, 0.8))
-    ax2 = fig.add_axes((0.1, 0.1, 0.34, 0.8))
-    ax3 = fig.add_axes((0.1, 0.1, 0.34, 0.8))
+    ax1_root = fig.add_axes((0, 0, 0.32, 1))
+    ax2_root = fig.add_axes((0.32, 0, 0.34, 1))
+    ax3_root = fig.add_axes((0.66, 0, 0.34, 1))
+    ax1 = fig.add_axes((0.03, 0.1, 0.23, 0.8))
+    ax2 = fig.add_axes((0.35, 0.1, 0.27, 0.8))
+    ax3 = fig.add_axes((0.69, 0.1, 0.27, 0.8))
 
     # Panel A
     logger.info("Plotting read kmer histogram")
 
     # Panel B
     logger.info("Plotting genetic map concordance")
+    draw_geneticmap_heatmap(ax2_root, ax2, mstmap, 1000)
 
     # Panel C
     logger.info("Plotting Hi-C contact map concordance")
 
-    labels = ((0.05, 0.95, "A"), (0.37, 0.95, "B"), (0.71, 0.95, "C"))
+    labels = ((0.05, 0.95, "A"), (0.35, 0.95, "B"), (0.7, 0.95, "C"))
     panel_labels(root, labels)
-    normalize_axes([root, ax1, ax2, ax3])
+    normalize_axes([root, ax1_root, ax2_root, ax3_root, ax1, ax2, ax3])
 
     image_name = "genomebuild.pdf"
     savefig(image_name, dpi=iopts.dpi, iopts=iopts)