Merge pull request #1581 from sschmeier/fix_cnv_plotting

Fixes the python plotting routines.

Author: pd3

vcfcnv.c

@@ -346,7 +346,7 @@ static void plot_sample(args_t *args, sample_t *smpl)
             "        chr = row[0]\n"
             "        if chr[0]=='#': continue\n"
             "        if chr not in dat: dat[chr] = []\n"
-            "        dat[chr].append([row[1], float(row[2]), float(row[3])])\n"
+            "        dat[chr].append([int(row[1]), float(row[2]), float(row[3])])\n"
             "\n"
             "cnv = {}\n"
             "with open('%s', 'r') as f:\n"
@@ -356,6 +356,7 @@ static void plot_sample(args_t *args, sample_t *smpl)
             "        if chr[0]=='#': continue\n"
             "        if chr not in cnv: cnv[chr] = []\n"
             "        row[2] = int(row[2]) + 0.5\n"
+            "        row[1] = int(row[1])\n"
             "        cnv[chr].append(row[1:])\n"
             "\n"
             "for chr in dat:\n"
@@ -372,7 +373,7 @@ static void plot_sample(args_t *args, sample_t *smpl)
             "       heat[1][x] = cn_dat[x][3]\n"
             "       heat[2][x] = cn_dat[x][4]\n"
             "       heat[3][x] = cn_dat[x][5]\n"
-            "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n"
+            "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r', shading='auto', alpha=0)\n"
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'.-',ms=3,color='black')\n"
             "    fig.suptitle('%s (chr '+chr+')')\n"
@@ -458,14 +459,15 @@ static void create_plots(args_t *args)
             "       for row in reader:\n"
             "           chr = row[0]\n"
             "           if chr != plot_chr: continue\n"
-            "           dat.append([row[1], float(row[2]), float(row[3])])\n"
+            "           dat.append([int(row[1]), float(row[2]), float(row[3])])\n"
             "def read_cnv(file,cnv,plot_chr):\n"
             "   with open(file, 'r') as f:\n"
             "       reader = csv.reader(f, 'tab')\n"
             "       for row in reader:\n"
             "           chr = row[0]\n"
             "           if chr != plot_chr: continue\n"
             "           row[2] = int(row[2]) + 0.5\n"
+            "           row[1] = int(row[1])\n"
             "           cnv.append(row[1:])\n"
             "def find_diffs(a,b):\n"
             "    out = []\n"
@@ -504,7 +506,7 @@ static void create_plots(args_t *args)
             "       heat[1][x] = cn_dat[x][3]\n"
             "       heat[2][x] = cn_dat[x][4]\n"
             "       heat[3][x] = cn_dat[x][5]\n"
-            "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr')\n"
+            "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr', shading='auto', alpha=0)\n"
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
             "\n"