def list_or_files(*args):
"""
Return the contents of *args as dict[name] = list pairs regardless of whether the user provided a filename or dict
If a list is provided, it will be appended to the dict with key ''
Returns a dict of name->list pairs
WARNING: This function uses base names, not the full path! If the base names are the same, one will be ignored!
"""
ndict = {}
for lst in args:
if isinstance(lst, list):
ndict.setdefault('', []).extend(lst)
print("WARNING: List received! Multiple lists are concatenated!")
elif isinstance(lst, dict):
ndict.update(lst)
else:
name = os.path.basename(lst)
ndict[name] = parsers.get_list_from_file(lst)
return ndict
def km(timeconv, eventconv, *clusts):
"""
Draw the kaplan-meier curves for a number of clusters
timeconv - file of tab-delim table of sample id -> survival time conversions
eventconv - file of tab-delim table of sample id -> event conversions (ie, 1 for yes, 0 for no, anything else for NA)
clusts - cluster filenames
"""
tc = parsers.read_table(timeconv)
ec = parsers.read_table(eventconv)
labels = []
times = []
events = []
for clust in clusts:
cl = parsers.get_list_from_file(clust)
ts = []
ev = []
for sam in cl:
try:
time = float(tc[sam])
event = int(ec[sam])
ts.append(time)
ev.append(event)
except:
pass
labels.append(clust)
times.append(ts)
events.append(ev)
display.km(times, events, labels)