def plot_vcf_comp(tsv_path, options):
""" take the big vcf compare table and make precision_recall plots for all the categories"""
out_dir = os.path.join(options.comp_dir, "comp_plots")
robust_makedirs(out_dir)
out_name = os.path.basename(os.path.splitext(tsv_path)[0])
out_base_path = os.path.join(out_dir, out_name)
region = out_name.split("-")[-1].upper()
out_base_path_f1 = os.path.join(out_dir, "-".join(out_name.split("-")[:-1]) + "--f1-" + region)
params = " ".join(PLOT_PARAMS)
# precision recall scatter plot
header = vcf_dist_header(options)
# strip qual
header = header[:-1]
for i in range(len(header) / 2):
prec_idx = 2 * i
rec_idx = prec_idx + 1
qual_idx = len(header)
print prec_idx, header[prec_idx], rec_idx, header[rec_idx]
ptoks = header[prec_idx].split("-")
rtoks = header[rec_idx].split("-")
assert ptoks[1] == "Precision"
assert rtoks[1] == "Recall"
assert ptoks[:1] == rtoks[:1]
comp_cat = ptoks[0]
if comp_cat not in ["TOT", "SNP", "INDEL"]:
continue
label = header[prec_idx].replace("Precision", "acc")
acc_tsv = out_base_path + "_" + label + ".tsv"
print "Make {} tsv with cols {} {}".format(label, rec_idx, prec_idx)
# +1 to convert to awk 1-base coordinates. +1 again since header doesnt include row_label col
awkcmd = '''if (NR!=1) print $1 "\t" ${} "\t" ${} "\t" ${}'''.format(rec_idx + 2, prec_idx + 2, qual_idx + 2)
awkstr = "awk \'{" + awkcmd + "}\'"
run("{} {} > {}".format(awkstr, tsv_path, acc_tsv))
acc_png = out_base_path + "_" + label + ".png"
title = "VCF"
if comp_cat == "TOT":
title += " Total Accuracy"
else:
title += " {} Accuracy".format(comp_cat)
title += " for {}".format(region)
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x -0.01 --max_x 1.01 --min_y -0.01 --max_y 1.01".format(acc_tsv, acc_png, title, params)
print cmd
os.system(cmd)
#flatten to max f1 tsv and plot as bars
f1_tsv = out_base_path_f1 + "_" + label + ".tsv"
f1_png = out_base_path_f1 + "_" + label + ".png"
f1_pr_tsv = out_base_path_f1.replace("-f1-", "-f1--pr-") + "_" + label + ".tsv"
f1_pr_png = out_base_path_f1.replace("-f1-", "-f1--pr-") + "_" + label + ".png"
f1_qual_tsv = out_base_path_f1.replace("-f1-", "-f1-qual-") + "_" + label + ".tsv"
f1_qual_png = out_base_path_f1.replace("-f1-", "-f1-qual-") + "_" + label + ".png"
make_max_f1_tsv(acc_tsv, f1_tsv, f1_pr_tsv, f1_qual_tsv, options)
cmd = "scripts/barchart.py {} --save {} --title \"{}\" --x_sideways --x_label \"Graph\" --y_label \"Max F1\" {}".format(f1_tsv, f1_png, title, params)
print cmd
os.system(cmd)
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x -0.01 --max_x 1.01 --min_y -0.01 --max_y 1.01".format(f1_pr_tsv, f1_pr_png, title, params)
print cmd
os.system(cmd)
cmd = "scripts/barchart.py {} --save {} --title \"{}\" --x_sideways --x_label \"Graph\" --y_label \"Quality for Max F1\" {} --max 20".format(f1_qual_tsv, f1_qual_png, title, params)
print cmd
os.system(cmd)
if options.top is True:
# top 20
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.798 --max_x 1.002 --min_y 0.798 --max_y 1.002".format(acc_tsv, acc_png.replace(".png", "_top20.png"), title, params)
print cmd
os.system(cmd)
# top 20
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 11 --height 5.5 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.796 --max_x 1.004 --min_y 0.796 --max_y 1.004".format(acc_tsv, acc_png.replace(".png", "_top20_inset.png"), title, params)
print cmd
os.system(cmd)
# top 40
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.596 --max_x 1.004 --min_y 0.596 --max_y 1.004".format(acc_tsv, acc_png.replace(".png", "_top40.png"), title, params)
print cmd
os.system(cmd)
def plot_vcf_comp(tsv_path, options):
""" take the big vcf compare table and make precision_recall plots for all the categories"""
out_dir = os.path.join(options.comp_dir, "comp_plots")
robust_makedirs(out_dir)
out_name = os.path.basename(os.path.splitext(tsv_path)[0])
sample = out_name.split("-")[-1].upper()
region = out_name.split("-")[-2].upper()
def out_base_path(tag, label, extension):
bd = tag if extension != ".tsv" else "tsv"
ret = os.path.join(out_dir, bd, "-".join(out_name.split("-")[:-1]) + "-{}-{}-".format(sample, tag) + region) + "_" + label + extension
robust_makedirs(os.path.dirname(ret))
return ret
params = " ".join(PLOT_PARAMS)
# precision recall scatter plot
header = vcf_dist_header(options)
# strip qual
header = header[:-1]
for i in range(len(header) / 2):
prec_idx = 2 * i
rec_idx = prec_idx + 1
qual_idx = len(header)
print prec_idx, header[prec_idx], rec_idx, header[rec_idx]
ptoks = header[prec_idx].split("-")
rtoks = header[rec_idx].split("-")
assert ptoks[1] == "Precision"
assert rtoks[1] == "Recall"
assert ptoks[:1] == rtoks[:1]
comp_cat = ptoks[0]
if comp_cat not in ["TOT", "SNP", "INDEL"]:
continue
label = header[prec_idx].replace("Precision", "acc")
acc_tsv = out_base_path("pr", label, ".tsv")
print "Make {} tsv with cols {} {}".format(label, rec_idx, prec_idx)
# +1 to convert to awk 1-base coordinates. +1 again since header doesnt include row_label col
awkcmd = '''if (NR!=1) print $1 "\t" ${} "\t" ${} "\t" ${}'''.format(rec_idx + 2, prec_idx + 2, qual_idx + 2)
awkstr = "awk \'{" + awkcmd + "}\'"
run("{} {} > {}".format(awkstr, tsv_path, acc_tsv))
acc_png = out_base_path("pr", label, ".png")
title = sample.upper() + " "
if comp_cat == "TOT":
title += " Total Accuracy"
else:
title += " {} Accuracy".format(comp_cat.title())
if region == "TOTAL":
title += ", all regions"
else:
title += ", {}".format(region)
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x -0.01 --max_x 1.01 --min_y -0.01 --max_y 1.01".format(acc_tsv, acc_png, title, params)
print cmd
os.system(cmd)
#flatten to max f1 tsv and plot as bars
f1_tsv = out_base_path("f1bar", label, ".tsv")
f1_png = out_base_path("f1bar", label, ".png")
f1_pr_tsv = out_base_path("f1pr", label, ".tsv")
f1_pr_png = out_base_path("f1pr", label, ".png")
f1_qual_tsv = out_base_path("f1qual", label, ".tsv")
f1_qual_png = out_base_path("f1qual", label, ".png")
make_max_f1_tsv(acc_tsv, f1_tsv, f1_pr_tsv, f1_qual_tsv, options)
cmd = "scripts/barchart.py {} --ascending --no_n --save {} --title \"{}\" --x_sideways --x_label \"Graph\" --y_label \"Max F1\" {}".format(f1_tsv, f1_png, title, params)
print cmd
os.system(cmd)
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5".format(f1_pr_tsv, f1_pr_png, title, params)
print cmd
os.system(cmd)
cmd = "scripts/barchart.py {} --ascending --no_n --save {} --title \"{}\" --x_sideways --x_label \"Graph\" --y_label \"Quality for Max F1\" {}".format(f1_qual_tsv, f1_qual_png, title, params)
print cmd
os.system(cmd)
if options.top is True:
# top 20
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.798 --max_x 1.002 --min_y 0.798 --max_y 1.002".format(acc_tsv, acc_png.replace(".png", "_top20.png"), title, params)
print cmd
os.system(cmd)
# top 20
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 11 --height 5.5 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.796 --max_x 1.004 --min_y 0.796 --max_y 1.004".format(acc_tsv, acc_png.replace(".png", "_top20_inset.png"), title, params)
print cmd
os.system(cmd)
# top 40
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.596 --max_x 1.004 --min_y 0.596 --max_y 1.004".format(acc_tsv, acc_png.replace(".png", "_top40.png"), title, params)
print cmd
os.system(cmd)
# top .5 bar
cmd = "scripts/barchart.py {} --ascending --no_n --save {} --title \"{}\" --x_sideways --x_label \"Graph\" --y_label \"Max F1\" {} --min 0.5".format(f1_tsv, f1_png.replace(".png", "_top50.png"), title, params)
print cmd
os.system(cmd)
# top .6 bar
cmd = "scripts/barchart.py {} --ascending --no_n --save {} --title \"{}\" --x_sideways --x_label \"Graph\" --y_label \"Max F1\" {} --min 0.6".format(f1_tsv, f1_png.replace(".png", "_top60.png"), title, params)
print cmd
os.system(cmd)
# top .7 bar
cmd = "scripts/barchart.py {} --ascending --no_n --save {} --title \"{}\" --x_sideways --x_label \"Graph\" --y_label \"Max F1\" {} --min 0.7".format(f1_tsv, f1_png.replace(".png", "_top70.png"), title, params)
print cmd
os.system(cmd)
# top .85 bar
cmd = "scripts/barchart.py {} --ascending --no_n --save {} --title \"{}\" --x_sideways --x_label \"Graph\" --y_label \"Max F1\" {} --min 0.85".format(f1_tsv, f1_png.replace(".png", "_top85.png"), title, params)
print cmd
os.system(cmd)
# top .25 f1pr scatter
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.746 --max_x 1.004 --min_y 0.746 --max_y 1.004".format(f1_pr_tsv, f1_pr_png.replace(".png", "_top25.png"), title, params)
print cmd
os.system(cmd)
# top .50 f1pr scatter
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.496 --max_x 1.004 --min_y 0.496 --max_y 1.004".format(f1_pr_tsv, f1_pr_png.replace(".png", "_top50.png"), title, params)
print cmd
os.system(cmd)
# top .65 f1pr scatter
cmd = "scripts/scatter.py {} --save {} --title \"{}\" --x_label \"Recall\" --y_label \"Precision\" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.646 --max_x 1.004 --min_y 0.646 --max_y 1.004".format(f1_pr_tsv, f1_pr_png.replace(".png", "_top65.png"), title, params)
print cmd
os.system(cmd)
def plot_vcf_comp(tsv_path, options):
""" take the big vcf compare table and make precision_recall plots for all the categories"""
out_dir = os.path.join(options.comp_dir, "comp_plots")
robust_makedirs(out_dir)
out_name = os.path.basename(os.path.splitext(tsv_path)[0])
sample = out_name.split("-")[-1].upper()
region = out_name.split("-")[-2].upper()
def out_base_path(tag, label, extension):
bd = tag if extension != ".tsv" else "tsv"
ret = (
os.path.join(out_dir, bd, "-".join(out_name.split("-")[:-1]) + "-{}-{}-".format(sample, tag) + region)
+ "_"
+ label
+ extension
)
robust_makedirs(os.path.dirname(ret))
return ret
params = " ".join(PLOT_PARAMS)
# precision recall scatter plot
header = vcf_dist_header(options)
# strip qual
header = header[:-1]
for i in range(len(header) / 2):
prec_idx = 2 * i
rec_idx = prec_idx + 1
qual_idx = len(header)
print prec_idx, header[prec_idx], rec_idx, header[rec_idx]
ptoks = header[prec_idx].split("-")
rtoks = header[rec_idx].split("-")
assert ptoks[1] == "Precision"
assert rtoks[1] == "Recall"
assert ptoks[:1] == rtoks[:1]
comp_cat = ptoks[0]
if comp_cat not in ["TOT", "SNP", "INDEL"]:
continue
label = header[prec_idx].replace("Precision", "acc")
acc_tsv = out_base_path("pr", label, ".tsv")
print "Make {} tsv with cols {} {}".format(label, rec_idx, prec_idx)
# +1 to convert to awk 1-base coordinates. +1 again since header doesnt include row_label col
awkcmd = """if (NR!=1) print $1 "\t" ${} "\t" ${} "\t" ${}""".format(rec_idx + 2, prec_idx + 2, qual_idx + 2)
awkstr = "awk '{" + awkcmd + "}'"
run("{} {} > {}".format(awkstr, tsv_path, acc_tsv))
acc_png = out_base_path("pr", label, ".png")
title = sample.upper() + " "
if comp_cat == "TOT":
title += " Total Accuracy"
else:
title += " {} Accuracy".format(comp_cat.title())
if region == "TOTAL":
title += ", all regions"
else:
title += ", {}".format(region)
cmd = 'scripts/scatter.py {} --save {} --title "{}" --x_label "Recall" --y_label "Precision" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x -0.01 --max_x 1.01 --min_y -0.01 --max_y 1.01'.format(
acc_tsv, acc_png, title, params
)
print cmd
os.system(cmd)
# flatten to max f1 tsv and plot as bars
f1_tsv = out_base_path("f1bar", label, ".tsv")
f1_png = out_base_path("f1bar", label, ".png")
f1_pr_tsv = out_base_path("f1pr", label, ".tsv")
f1_pr_png = out_base_path("f1pr", label, ".png")
f1_qual_tsv = out_base_path("f1qual", label, ".tsv")
f1_qual_png = out_base_path("f1qual", label, ".png")
make_max_f1_tsv(acc_tsv, f1_tsv, f1_pr_tsv, f1_qual_tsv, options)
cmd = 'scripts/barchart.py {} --ascending --no_n --save {} --title "{}" --x_sideways --x_label "Graph" --y_label "Max F1" {}'.format(
f1_tsv, f1_png, title, params
)
print cmd
os.system(cmd)
cmd = 'scripts/scatter.py {} --save {} --title "{}" --x_label "Recall" --y_label "Precision" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5'.format(
f1_pr_tsv, f1_pr_png, title, params
)
print cmd
os.system(cmd)
cmd = 'scripts/barchart.py {} --ascending --no_n --save {} --title "{}" --x_sideways --x_label "Graph" --y_label "Quality for Max F1" {}'.format(
f1_qual_tsv, f1_qual_png, title, params
)
print cmd
os.system(cmd)
if options.top is True:
# top 20
cmd = 'scripts/scatter.py {} --save {} --title "{}" --x_label "Recall" --y_label "Precision" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.798 --max_x 1.002 --min_y 0.798 --max_y 1.002'.format(
acc_tsv, acc_png.replace(".png", "_top20.png"), title, params
)
print cmd
os.system(cmd)
# top 20
cmd = 'scripts/scatter.py {} --save {} --title "{}" --x_label "Recall" --y_label "Precision" --width 11 --height 5.5 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.796 --max_x 1.004 --min_y 0.796 --max_y 1.004'.format(
acc_tsv, acc_png.replace(".png", "_top20_inset.png"), title, params
)
print cmd
os.system(cmd)
# top 40
cmd = 'scripts/scatter.py {} --save {} --title "{}" --x_label "Recall" --y_label "Precision" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.596 --max_x 1.004 --min_y 0.596 --max_y 1.004'.format(
acc_tsv, acc_png.replace(".png", "_top40.png"), title, params
)
print cmd
os.system(cmd)
# top .5 bar
cmd = 'scripts/barchart.py {} --ascending --no_n --save {} --title "{}" --x_sideways --x_label "Graph" --y_label "Max F1" {} --min 0.5'.format(
f1_tsv, f1_png.replace(".png", "_top50.png"), title, params
)
print cmd
os.system(cmd)
# top .6 bar
cmd = 'scripts/barchart.py {} --ascending --no_n --save {} --title "{}" --x_sideways --x_label "Graph" --y_label "Max F1" {} --min 0.6'.format(
f1_tsv, f1_png.replace(".png", "_top60.png"), title, params
)
print cmd
os.system(cmd)
# top .7 bar
cmd = 'scripts/barchart.py {} --ascending --no_n --save {} --title "{}" --x_sideways --x_label "Graph" --y_label "Max F1" {} --min 0.7'.format(
f1_tsv, f1_png.replace(".png", "_top70.png"), title, params
)
print cmd
os.system(cmd)
# top .85 bar
cmd = 'scripts/barchart.py {} --ascending --no_n --save {} --title "{}" --x_sideways --x_label "Graph" --y_label "Max F1" {} --min 0.85'.format(
f1_tsv, f1_png.replace(".png", "_top85.png"), title, params
)
print cmd
os.system(cmd)
# top .25 f1pr scatter
cmd = 'scripts/scatter.py {} --save {} --title "{}" --x_label "Recall" --y_label "Precision" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.746 --max_x 1.004 --min_y 0.746 --max_y 1.004'.format(
f1_pr_tsv, f1_pr_png.replace(".png", "_top25.png"), title, params
)
print cmd
os.system(cmd)
# top .50 f1pr scatter
cmd = 'scripts/scatter.py {} --save {} --title "{}" --x_label "Recall" --y_label "Precision" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.496 --max_x 1.004 --min_y 0.496 --max_y 1.004'.format(
f1_pr_tsv, f1_pr_png.replace(".png", "_top50.png"), title, params
)
print cmd
os.system(cmd)
# top .65 f1pr scatter
cmd = 'scripts/scatter.py {} --save {} --title "{}" --x_label "Recall" --y_label "Precision" --width 18 --height 9 {} --lines --no_n --line_width 1.5 --marker_size 5 --min_x 0.646 --max_x 1.004 --min_y 0.646 --max_y 1.004'.format(
f1_pr_tsv, f1_pr_png.replace(".png", "_top65.png"), title, params
)
print cmd
os.system(cmd)
