def func_detailed_viz(infile_rank_tree,
infile_average,
infile_filtered,
detailed_pdf,
tempdir,
docker_image=None):
infile_filtered = os.path.abspath(infile_filtered)
infile_average = os.path.abspath(infile_average)
infile_rank_tree = os.path.abspath(infile_rank_tree)
cmd = (
'xvfb-run',
'corrupt-viz-growth',
'--experimentConfigs.saveStandardStreams',
'false',
'--experimentConfigs.recordGitInfo',
'false',
'--experimentConfigs.managedExecutionFolder',
'false',
'--phylogenies',
infile_rank_tree,
'--matrices',
infile_average,
infile_filtered,
'--size',
'width',
'300',
)
run_in_dir(cmd, [], [], tempdir, docker_image=docker_image)
pdffiles = glob.glob('{}/*.pdf'.format(tempdir))
pdfutils.merge_pdfs(pdffiles, detailed_pdf)
def plot_kernel_density(infile, output, tempdir, sep, colname, plot_title,
multipliers):
helpers.makedirs(tempdir)
multiplier_pdfs = []
for multiplier in multipliers:
multiplier_output = os.path.join(tempdir, "{}.pdf".format(multiplier))
multiplier_pdfs.append(multiplier_output)
mult_plot_title = '{}({})'.format(plot_title, multiplier)
tablename = '/hmmcopy/metrics/{}'.format(multiplier)
plot = PlotKernelDensity(infile,
multiplier_output,
sep,
colname,
mult_plot_title,
tablename=tablename)
plot.main()
pdfutils.merge_pdfs(multiplier_pdfs, output)
def plot_pcolor(infile,
metrics,
output,
tempdir,
multipliers,
plot_title=None,
column_name=None,
plot_by_col=None,
chromosomes=None,
max_cn=None,
scale_by_cells=None,
color_by_col=None,
cell_filters=None,
mappability_threshold=None):
helpers.makedirs(tempdir)
multiplier_pdfs = []
for multiplier in multipliers:
cells = get_good_cells(metrics, cell_filters, '/hmmcopy/metrics/0')
multiplier_output = os.path.join(tempdir, "{}.pdf".format(multiplier))
multiplier_pdfs.append(multiplier_output)
mult_plot_title = '{}({})'.format(plot_title, multiplier)
reads_tablename = '/hmmcopy/reads/{}'.format(multiplier)
metrics_tablename = '/hmmcopy/metrics/{}'.format(multiplier)
plot = PlotPcolor(infile,
metrics,
multiplier_output,
plot_title=mult_plot_title,
column_name=column_name,
plot_by_col=plot_by_col,
chromosomes=chromosomes,
max_cn=max_cn,
multiplier=multiplier,
scale_by_cells=scale_by_cells,
segs_tablename=reads_tablename,
metrics_tablename=metrics_tablename,
color_by_col=color_by_col,
cells=cells,
mappability_threshold=mappability_threshold)
plot.main()
pdfutils.merge_pdfs(multiplier_pdfs, output)
def plot_metrics(metrics, output, tempdir, plot_title, multipliers):
helpers.makedirs(tempdir)
multiplier_pdfs = []
for multiplier in multipliers:
multiplier_output = os.path.join(tempdir, "{}.pdf".format(multiplier))
multiplier_pdfs.append(multiplier_output)
mult_plot_title = '{}({})'.format(plot_title, multiplier)
tablename = '/hmmcopy/metrics/{}'.format(multiplier)
plot = PlotMetrics(metrics,
multiplier_output,
mult_plot_title,
tablename=tablename)
plot.plot_hmmcopy_metrics()
pdfutils.merge_pdfs(multiplier_pdfs, output)
def merge_pdf(in_filenames, out_filename):
for in_files, out_file in zip(in_filenames, out_filename):
pdfutils.merge_pdfs(in_files, out_file)