def clustering(self, dist=10):
"""Handle data for finding clusters of cells."""
kws = {'Dist': dist} # Maximum distance for considering clustering
data = None
# Listing of paths of channels on which clusters are to be found
cluster_chans = [
p for p in self.channelPaths for t in Sett.cluster_channels
if t.lower() == p.stem.lower()
]
for path in cluster_chans: # Loop paths, read file, and find clusters
try:
data = system.read_data(path, header=0)
except (FileNotFoundError, AttributeError):
msg = "No file for channel {}".format(path.stem)
lg.logprint(LAM_logger, "{}: {}".format(self.name, msg), 'w')
print("-> {}".format(msg))
# Discard earlier versions of found clusters, if present
if data is not None:
data = data.loc[:, ~data.columns.str.contains('ClusterID')]
data.name = path.stem # The name of the clustering channel
# Find clusters
self.find_distances(data,
vol_incl=Sett.cl_inclusion,
compare=Sett.cl_incl_type,
clusters=True,
**kws)
def get_mps(self, mp_name: str, use_mp: bool,
datadir: pl.Path) -> pd.Series:
"""Collect MPs for sample anchoring."""
if use_mp:
try: # Get measurement point for anchoring
mp_dir_path = next(
self.channelpaths.pop(i)
for i, s in enumerate(self.channelpaths)
if str('_' + mp_name + '_') in str(s))
mp_path = next(mp_dir_path.glob("*Position.csv"))
mp_data = system.read_data(mp_path,
header=Sett.header_row,
test=False)
mp_data = mp_data.loc[:, ['Position X', 'Position Y']]
if not mp_data.empty:
mp_bin = self.project_mps(mp_data,
datadir,
filename="MPs.csv")
mp_df = pd.DataFrame({'MP': mp_bin.values.codes})
mp_df.to_csv(self.sampledir.joinpath("MPs.csv"),
index=False)
except (StopIteration, ValueError, UnboundLocalError):
mp_bin = None
msg = f'could not find MP position for {self.name}'
lg.logprint(LAM_logger, msg, 'e')
print(" -> Failed to find MP position data.")
else: # Sets measurement point values to zero when MP's are not used
mp_bin = pd.Series(0, name=self.name)
system.save_to_file(mp_bin, datadir, "MPs.csv")
system.save_to_file(mp_bin,
self.sampledir,
"MPs.csv",
append=False)
return mp_bin
def __init__(self, paths=None, child=False):
if child:
return
# Creation of variables related to all samples, that are later passed
# on to child classes.
Samplegroups._groups = sorted(Store.samplegroups)
Samplegroups._chanPaths = list(paths.datadir.glob('Norm_*'))
Samplegroups.sample_paths = [
p for p in paths.samplesdir.iterdir() if p.is_dir()
]
Samplegroups._addData = list(paths.datadir.glob('Avg_*'))
# Data and other usable directories
Samplegroups.paths = paths
# Total length of needed data matrix of all anchored samples
Samplegroups.bin_length = Store.totalLength
# Get MPs of all samples
mp_path = paths.datadir.joinpath('MPs.csv')
Samplegroups.sample_mps = system.read_data(mp_path,
header=0,
test=False)
# If anchor point index is defined, find the start index of samples
if Store.center is not None:
Samplegroups.center_bin = Store.center
# Assign color for each sample group
groupcolors = sns.xkcd_palette(Sett.palette_colors)
for i, grp in enumerate(Samplegroups._groups):
Samplegroups.grp_palette.update({grp: groupcolors[i]})
lg.logprint(LAM_logger, 'Sample groups established.', 'i')
def avg_add_data(self, paths: system.Paths, data_names: dict,
total_len: int):
"""Find bin averages of additional data."""
samples = self.starts.index
for sample in samples:
sample_dir = paths.samplesdir.joinpath(sample)
data_file = sample_dir.glob(str(self.channel + '.csv'))
data = system.read_data(next(data_file), header=0)
for data_type in data_names.keys():
sample_data = data.loc[:,
data.columns.str.contains(str(data_type)
)]
if sample_data.empty:
continue
binned_data = data.loc[:, 'DistBin']
bins = np.arange(0, Sett.projBins)
for col in sample_data:
avg_s = pd.Series(np.full(total_len, np.nan), name=sample)
with warnings.catch_warnings():
warnings.simplefilter('ignore',
category=RuntimeWarning)
insert = [
np.nanmean(sample_data.loc[binned_data == i, col])
for i in bins
]
insert = [0 if np.isnan(v) else v for v in insert]
start = int(self.starts.at[sample])
end = int(start + Sett.projBins)
avg_s[start:end] = insert
filename = str('Avg_{}_{}.csv'.format(self.channel, col))
system.save_to_file(avg_s, paths.datadir, filename)
def distance_mean(self, dist=25):
"""Prepare and handle data for cell-to-cell distances."""
kws = {'Dist': dist} # Maximum distance used to find cells
# List paths of channels where distances are to be found
dist_chans = [
p for p in self.channelPaths for t in Sett.distance_channels
if t.lower() == p.stem.lower()
]
if Sett.use_target: # If distances are found against other channel:
target = Sett.target_chan # Get the name of the target channel
try: # Find target's data file, read, and update data to keywords
file = '{}.csv'.format(target)
test_namer = re.compile(file, re.I)
target_path = [
p for p in self.channelPaths
if test_namer.fullmatch(str(p.name))
]
test_data = system.read_data(target_path[0], header=0)
kws.update({'test_data': test_data})
except (FileNotFoundError, IndexError):
msg = "No file for channel {}".format(target)
lg.logprint(LAM_logger, "{}: {}".format(self.name, msg), 'w')
print("-> {}".format(msg))
return
# Loop through the channels, read, and find distances
for path in dist_chans:
try:
data = system.read_data(path, header=0)
except FileNotFoundError:
msg = "No file for channel {}".format(path.stem)
lg.logprint(LAM_logger, "{}: {}".format(self.name, msg), 'w')
print("-> {}".format(msg))
return
# Discard earlier versions of calculated distances, if present
data = data.loc[:, ~data.columns.str.startswith('Nearest_')]
# Find distances
data.name = path.stem
self.find_distances(data,
vol_incl=Sett.inclusion,
compare=Sett.incl_type,
**kws)
def read_channel(self, path):
"""Read channel data into a dataframe."""
try:
data = system.read_data(str(path), header=Sett.header_row)
channel = self.name
if channel.lower() not in [
c.lower() for c in Store.channels
] and channel.lower() != Sett.MPname.lower():
Store.channels.append(self.name)
return data
except ValueError:
lg.logprint(LAM_logger, 'Cannot read channel path {}'.format(path),
'ex')
def __init__(self, path, groups, plot_dir, stat_dir):
self.dataerror = False
self.error_vars = {}
self.plot_dir = plot_dir
self.stat_dir = stat_dir
self.filename = path.stem
self.data = system.read_data(path, header=0, test=False, index_col=0)
# Test that data exists
if self.data is None or self.data.empty:
self.dataerror = True
self.groups = groups
self.test_grps = [g for g in groups if g != Sett.cntrlGroup]
self.stat_data = None
def mww_test(self, channel_path):
"""Perform MWW-test for a data set of two groups."""
self.error = False
self.channel = ' '.join(str(channel_path.stem).split('_')[1:])
data = system.read_data(channel_path, header=0, test=False)
# Test that data exists and has non-zero numeric values
cols = data.any().index
valid_data = data.loc[:, cols]
valid_grp_n = cols.map(lambda x: str(x).split('_')[0]).unique().size
if not valid_data.any().any() or valid_grp_n < 2:
self.error = True
# Find group-specific data
grp_data = valid_data.T.groupby(lambda x: str(x).split('_')[0])
try:
self.ctrl_data = grp_data.get_group(self.ctrl_grp).T
self.test_data = grp_data.get_group(self.test_grp).T
except KeyError: # If sample group not found, i.e. no sample has data
self.error = True
if self.error:
print(f"WARNING: {self.channel} - Insufficient data, skipped.")
stat_cols = [
'U Score', 'Corr. Greater', 'P Greater', 'Reject Greater',
'Corr. Lesser', 'P Lesser', 'Reject Lesser', 'Corr. Two-sided',
'P Two-sided', 'Reject Two-sided'
]
stat_data = pd.DataFrame(index=data.index, columns=stat_cols)
if Sett.windowed: # If doing rolling window stats
stat_data = self.windowed_test(stat_data)
else: # Bin-by-bin stats:
stat_data = self.bin_test(stat_data)
# Correct for multiple testing:
stat_data = correct(stat_data, stat_data.iloc[:, 2], 1, 3) # greater
stat_data = correct(stat_data, stat_data.iloc[:, 5], 4, 6) # lesser
stat_data = correct(stat_data, stat_data.iloc[:, 8], 7, 9) # 2-sided
# Save statistics
filename = f'Stats_{self.title} = {self.channel}.csv'
system.save_to_file(stat_data, self.stat_dir, filename, append=False)
self.stat_data = stat_data
def get_vect_data(self, channel):
"""Get channel data that is used for vector creation."""
try:
# Search string:
namer = str("_{}_".format(channel))
namerreg = re.compile(namer, re.I)
# Search found paths with string
dir_path = [
self.channelpaths[i] for i, s in enumerate(self.channelpaths)
if namerreg.search(str(s))
][0]
vect_path = next(dir_path.glob('*Position.csv'))
vect_data = system.read_data(vect_path,
header=Sett.header_row) # Read data
except (FileNotFoundError, IndexError): # If data file not found
msg = 'No valid datafile for vector creation.'
if LAM_logger is not None:
lg.logprint(LAM_logger, msg, 'w')
print('-> {}'.format(msg))
vect_data = None
return vect_data
def read_channel(self, path, groups, drop=False, name_sep=1):
"""Read channel data and concatenate sample group info into DF."""
data = system.read_data(path, header=0, test=False)
read_data = pd.DataFrame()
# Loop through given groups and give an identification variable for
# each sample belonging to the group.
for grp in groups:
namerreg = re.compile('^{}_'.format(grp), re.I)
# Get only the samples that belong to the loop's current group
temp = data.loc[:, data.columns.str.contains(namerreg)].T
if Sett.Drop_Outliers and drop: # conditionfull_dfy drop outliers
temp = drop_outlier(temp)
temp['Sample Group'] = grp # Giving of sample group identification
if read_data.empty:
read_data = temp
else:
read_data = pd.concat([read_data, temp])
# Finding the name of the data under analysis from its filepath
name = '_'.join(str(path.stem).split('_')[name_sep:])
center = self.center_bin # Getting the bin to which samples are centered
return read_data, name, center
def get_widths(samplesdir, datadir):
"""Find widths of samples along their vectors."""
msg = "Necessary files for width approximation not found for "
data, vector_data = None, None
for path in [p for p in samplesdir.iterdir() if p.is_dir()]:
# Find necessary data files:
files = [p for p in path.iterdir() if p.is_file()]
# Search terms
vreg = re.compile('^vector.', re.I) # vector
dreg = re.compile(f'^{Sett.vectChannel}.csv', re.I) # channel data
try: # Match terms to found paths
vect_paths = [p for p in files if vreg.match(p.name)]
data_paths = [p for p in files if dreg.match(p.name)]
# Read found paths
vector_data = system.read_vector(vect_paths)
data = system.read_data(data_paths[0], header=0)
# Error handling
except (StopIteration, IndexError):
name = path.name
full_msg = msg + name
print(f"WARNING: {full_msg}")
if 'vector_data' not in locals(): # if vector not found
print("-> Could not read vector data.")
continue
if 'data' not in locals(): # if channel data not found
print("Could not read channel data")
print("Make sure channel is set right (vector channel)\n")
continue
lg.logprint(LAM_logger, full_msg, 'w')
# Compute widths
process.DefineWidths(data, vector_data, path, datadir)
def get_counts(paths):
"""Handle data to anchor samples and find cell counts."""
try: # Test that MPs are found for the sample
mps = system.read_data(next(paths.datadir.glob('MPs.csv')),
header=0,
test=False)
except (FileNotFoundError, StopIteration):
msg = "MPs.csv NOT found!"
print("ERROR: {}".format(msg))
lg.logprint(LAM_logger, msg, 'c')
msg = "-> Perform 'Count' before continuing.\n"
print("{}".format(msg))
lg.logprint(LAM_logger, msg, 'i')
raise SystemExit
# Find the smallest and largest anchor bin-number of the dataset
mp_max, mp_min = mps.max(axis=1).values[0], mps.min(axis=1).values[0]
# Store the bin number of the row onto which samples are anchored to
Store.center = mp_max
# Find the size of needed dataframe, i.e. so that all anchored samples fit
mp_diff = mp_max - mp_min
if not any([Sett.process_counts, Sett.process_samples]):
# Find all sample groups in the analysis from the found MPs.
found_samples = [p for p in paths.samplesdir.iterdir() if p.is_dir()]
samples = mps.columns.tolist()
if len(found_samples) != len(
samples): # Test whether sample numbers match
msg = "Mismatch of sample N between MPs.csv and sample folders"
print('WARNING: {}'.format(msg))
lg.logprint(LAM_logger, msg, 'w')
groups = set({s.casefold(): s.split('_')[0] for s in samples}.values())
Store.samplegroups = sorted(groups)
Store.channels = [
c.stem.split('_')[1] for c in paths.datadir.glob("All_*.csv")
]
try: # If required lengths of matrices haven't been defined because
# Process and Count are both False, get the sizes from files.
chan = Sett.vectChannel
path = paths.datadir.joinpath("Norm_{}.csv".format(chan))
temp = system.read_data(path, test=False, header=0)
Store.totalLength = temp.shape[0] # Length of anchored matrices
path = paths.datadir.joinpath("All_{}.csv".format(chan))
temp = system.read_data(path, test=False, header=0)
Sett.projBins = temp.shape[0]
except AttributeError:
msg = "Cannot determine length of sample matrix\n-> Must perform 'Count' before continuing."
lg.logprint(LAM_logger, msg, 'c')
print("ERROR: {}".format(msg))
return
# The total length of needed matrix when using 'Count'
Store.totalLength = int(Sett.projBins + mp_diff)
# Counting and anchoring of data:
if Sett.process_counts:
lg.logprint(LAM_logger, 'Begin normalization of channels.', 'i')
print('\n---Normalizing sample data---')
# Get combined channel files of all samples
countpaths = paths.datadir.glob('All_*')
for path in countpaths:
name = str(path.stem).split('_')[1]
print(' {} ...'.format(name))
# Anchor sample's data to the full data matrix
ch_counts = Normalize(path)
ch_counts.starts, norm_counts = ch_counts.normalize_samples(
mps, Store.totalLength, Store.center)
# Get average bin counts
ch_counts.averages(norm_counts)
# Get averages of additional data per bin
ch_counts.avg_add_data(paths, Sett.AddData, Store.totalLength)
# Approximate width of sample
if Sett.measure_width:
print(' Width ...')
width_path = paths.datadir.joinpath('Sample_widths.csv')
width_counts = Normalize(width_path)
_, _ = width_counts.normalize_samples(mps * 2,
Store.totalLength * 2,
Store.center * 2,
name='Sample_widths_norm')
lg.logprint(LAM_logger, 'Channels normalized.', 'i')
def __init__(self, path):
self.path = pl.Path(path)
self.channel = str(self.path.stem).split('_')[1]
self.counts = system.read_data(path, header=0, test=False)
self.starts = None
def read_additional(self, data_keys):
"""Read relevant additional data of channel."""
def _test_variance(data):
"""Test if additional data column contains variance."""
for column in data.columns.difference(['ID']):
test = data.loc[:, column].dropna()
test = (test - test.min()) / test.max()
if test.std() < 0.01:
self.datafail.append(column)
data.loc[:, column] = np.nan
return data
def _rename_id(data):
"""Rename filename identification of channel."""
# I.e. as defined by settings.channelID
for column in data.columns:
id_str = str(column).split('_')[-1]
if id_str in Sett.channelID.keys():
new_id = Sett.channelID.get(id_str)
data.rename(columns={
column:
column.replace(f'_{id_str}', f'-{new_id}')
},
inplace=True)
return data
add_data = pd.DataFrame(self.data.loc[:, 'ID'])
for key, values in data_keys.items():
paths = list(self.path.glob(f'*{values[0]}*'))
if not paths:
print(f"-> {self.name} {key} file not found")
continue
if len(paths) == 1:
namer = re.compile(f'^{key}', re.I)
if paths[0] == self.pospath and any(
self.data.columns.str.contains(namer)):
continue
if paths[0] == self.pospath and not any(
self.data.columns.str.contains(namer)):
print(
f"'{key}' not in {self.pospath.name} of {self.sample.name} on channel {self.name}"
)
temp_data = system.read_data(str(paths[0]),
header=Sett.header_row)
cols = temp_data.columns.map(lambda x, matcher=namer: bool(
re.match(matcher, x)) or x == 'ID')
temp_data = temp_data.loc[:, cols]
add_data = pd.merge(add_data, temp_data, on='ID')
else: # If multiple files, e.g. intensity, get all
for path in paths:
# Search identifier for column from filename
strings = str(path.stem).split(f'{values[0]}_')
id_string = strings[1].split('_')[0]
# Locate columns
temp_data = system.read_data(str(path),
header=Sett.header_row)
temp_data = temp_data.loc[:, [key, 'ID']]
for col in [c for c in temp_data.columns if c != 'ID']:
rename = str(col + '_' + id_string)
temp_data.rename(columns={key: rename}, inplace=True)
add_data = pd.merge(add_data, temp_data, on='ID')
# Drop invariant data
add_data = _test_variance(add_data)
if Sett.replaceID:
add_data = _rename_id(add_data)
self.data = pd.merge(self.data, add_data, on='ID')
