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rnaseqTools.py
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rnaseqTools.py
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import numpy as np
import pylab as plt
import seaborn as sns
import pandas as pd
from scipy import sparse
def sparseload(filename, sep=',', dtype=float, chunksize=1000, index_col=0, droplastcolumns=0):
with open(filename) as file:
genes = []
sparseblocks = []
for i,chunk in enumerate(pd.read_csv(filename, chunksize=chunksize, sep=sep, index_col=index_col)):
print('.', end='', flush=True)
if i==0:
cells = np.array(chunk.columns)
genes.extend(list(chunk.index))
sparseblock = sparse.csr_matrix(chunk.values.astype(dtype))
sparseblocks.append([sparseblock])
counts = sparse.bmat(sparseblocks)
print(' done')
if droplastcolumns > 0:
end = cells.size - droplastcolumns
cells = cells[:end]
counts = counts[:,:end]
return (counts.T, np.array(genes), cells)
def geneSelection(data, threshold=0, atleast=10,
yoffset=.02, xoffset=5, decay=1.5, n=None,
plot=True, markers=None, genes=None, figsize=(6,3.5),
markeroffsets=None, labelsize=10, alpha=1, verbose=1):
if sparse.issparse(data):
zeroRate = 1 - np.squeeze(np.array((data>threshold).mean(axis=0)))
A = data.multiply(data>threshold)
A.data = np.log2(A.data)
meanExpr = np.zeros_like(zeroRate) * np.nan
detected = zeroRate < 1
meanExpr[detected] = np.squeeze(np.array(A[:,detected].mean(axis=0))) / (1-zeroRate[detected])
else:
zeroRate = 1 - np.mean(data>threshold, axis=0)
meanExpr = np.zeros_like(zeroRate) * np.nan
detected = zeroRate < 1
mask = data[:,detected]>threshold
logs = np.zeros_like(data[:,detected]) * np.nan
logs[mask] = np.log2(data[:,detected][mask])
meanExpr[detected] = np.nanmean(logs, axis=0)
lowDetection = np.array(np.sum(data>threshold, axis=0)).squeeze() < atleast
zeroRate[lowDetection] = np.nan
meanExpr[lowDetection] = np.nan
if n is not None:
up = 10
low = 0
for t in range(100):
nonan = ~np.isnan(zeroRate)
selected = np.zeros_like(zeroRate).astype(bool)
selected[nonan] = zeroRate[nonan] > np.exp(-decay*(meanExpr[nonan] - xoffset)) + yoffset
if np.sum(selected) == n:
break
elif np.sum(selected) < n:
up = xoffset
xoffset = (xoffset + low)/2
else:
low = xoffset
xoffset = (xoffset + up)/2
if verbose>0:
print('Chosen offset: {:.2f}'.format(xoffset))
else:
nonan = ~np.isnan(zeroRate)
selected = np.zeros_like(zeroRate).astype(bool)
selected[nonan] = zeroRate[nonan] > np.exp(-decay*(meanExpr[nonan] - xoffset)) + yoffset
if plot:
if figsize is not None:
plt.figure(figsize=figsize)
plt.ylim([0, 1])
if threshold>0:
plt.xlim([np.log2(threshold), np.ceil(np.nanmax(meanExpr))])
else:
plt.xlim([0, np.ceil(np.nanmax(meanExpr))])
x = np.arange(plt.xlim()[0], plt.xlim()[1]+.1,.1)
y = np.exp(-decay*(x - xoffset)) + yoffset
if decay==1:
plt.text(.4, 0.2, '{} genes selected\ny = exp(-x+{:.2f})+{:.2f}'.format(np.sum(selected),xoffset, yoffset),
color='k', fontsize=labelsize, transform=plt.gca().transAxes)
else:
plt.text(.4, 0.2, '{} genes selected\ny = exp(-{:.1f}*(x-{:.2f}))+{:.2f}'.format(np.sum(selected),decay,xoffset, yoffset),
color='k', fontsize=labelsize, transform=plt.gca().transAxes)
plt.plot(x, y, color=sns.color_palette()[1], linewidth=2)
xy = np.concatenate((np.concatenate((x[:,None],y[:,None]),axis=1), np.array([[plt.xlim()[1], 1]])))
t = plt.matplotlib.patches.Polygon(xy, color=sns.color_palette()[1], alpha=.4)
plt.gca().add_patch(t)
plt.scatter(meanExpr, zeroRate, s=1, alpha=alpha, rasterized=True)
if threshold==0:
plt.xlabel('Mean log2 nonzero expression')
plt.ylabel('Frequency of zero expression')
else:
plt.xlabel('Mean log2 nonzero expression')
plt.ylabel('Frequency of near-zero expression')
plt.tight_layout()
if markers is not None and genes is not None:
if markeroffsets is None:
markeroffsets = [(0, 0) for g in markers]
for num,g in enumerate(markers):
i = np.where(genes==g)[0]
plt.scatter(meanExpr[i], zeroRate[i], s=10, color='k')
dx, dy = markeroffsets[num]
plt.text(meanExpr[i]+dx+.1, zeroRate[i]+dy, g, color='k', fontsize=labelsize)
return selected
# Computing the matrix of Euclidean distances
def pdist2(A,B):
D = np.sum(A**2,axis=1,keepdims=True) + np.sum(B**2, axis=1, keepdims=True).T - 2*[email protected]
return D
import warnings
# Computing the matrix of correlations
def corr2(A,B):
A = A - A.mean(axis=1, keepdims=True)
B = B - B.mean(axis=1, keepdims=True)
ssA = (A**2).sum(axis=1, keepdims=True)
ssB = (B**2).sum(axis=1, keepdims=True)
# this ignores the NaN warnings. The result can have nans!
with warnings.catch_warnings():
warnings.simplefilter('ignore')
C = np.dot(A, B.T) / np.sqrt(np.dot(ssA,ssB.T))
return C
def map_to_tsne(referenceCounts, referenceGenes, newCounts, newGenes, referenceAtlas,
bootstrap = False, knn = 10, nrep = 100, seed = None, batchsize = 1000,
verbose = 1):
gg = sorted(list(set(referenceGenes) & set(newGenes)))
if verbose > 0:
print('Using a common set of ' + str(len(gg)) + ' genes.')
newGenes = [np.where(newGenes==g)[0][0] for g in gg]
refGenes = [np.where(referenceGenes==g)[0][0] for g in gg]
X = newCounts[:,newGenes]
if sparse.issparse(X):
X = np.array(X.todense())
X = np.log2(X + 1)
T = referenceCounts[:,refGenes]
if sparse.issparse(T):
T = np.array(T.todense())
T = np.log2(T + 1)
n = X.shape[0]
assignmentPositions = np.zeros((n, referenceAtlas.shape[1]))
batchCount = int(np.ceil(n/batchsize))
if (batchCount > 1) and (verbose > 0):
print('Processing in batches', end='', flush=True)
for b in range(batchCount):
if (batchCount > 1) and (verbose > 0):
print('.', end='', flush=True)
batch = np.arange(b*batchsize, np.minimum((b+1)*batchsize, n))
C = corr2(X[batch,:], T)
ind = np.argpartition(C, -knn)[:, -knn:]
for i in range(batch.size):
assignmentPositions[batch[i],:] = np.median(referenceAtlas[ind[i,:],:], axis=0)
if (batchCount > 1) and (verbose > 0):
print(' done', flush=True)
# Note: currently bootstrapping does not support batchsize
if bootstrap:
if seed is not None:
np.random.seed(seed)
assignmentPositions_boot = np.zeros((n, referenceAtlas.shape[1], nrep))
if verbose>0:
print('Bootstrapping', end='', flush=True)
for rep in range(nrep):
if verbose>0:
print('.', end='')
bootgenes = np.random.choice(T.shape[1], T.shape[1], replace=True)
C_boot = corr2(X[:,bootgenes],T[:,bootgenes])
ind = np.argpartition(C_boot, -knn)[:, -knn:]
for i in range(X.shape[0]):
assignmentPositions_boot[i,:,rep] = np.median(referenceAtlas[ind[i,:],:], axis=0)
if verbose>0:
print(' done')
return (assignmentPositions, assignmentPositions_boot)
else:
return assignmentPositions
def map_to_clusters(referenceCounts, referenceGenes,
newCounts, newGenes,
referenceClusters, referenceClusterNames=[], cellNames=[],
bootstrap = False, nrep = 100, seed = None, verbose = False, until=.95,
returnCmeans = False, totalClusters = None):
gg = sorted(list(set(referenceGenes) & set(newGenes)))
print('Using a common set of ' + str(len(gg)) + ' genes.')
newGenes = [np.where(newGenes==g)[0][0] for g in gg]
refGenes = [np.where(referenceGenes==g)[0][0] for g in gg]
X = newCounts[:,newGenes]
if sparse.issparse(X):
X = np.array(X.todense())
X = np.log2(X + 1)
T = referenceCounts[:,refGenes]
if sparse.issparse(T):
T = np.array(T.todense())
T = np.log2(T + 1)
if totalClusters is not None:
K = totalClusters
else:
K = np.max(referenceClusters) + 1
means = np.zeros((K, T.shape[1]))
for c in range(K):
if np.sum(referenceClusters==c) > 0:
means[c,:] = np.mean(T[referenceClusters==c,:], axis=0)
Cmeans = corr2(X, means)
allnans = np.sum(np.isnan(Cmeans), axis=1) == Cmeans.shape[1]
clusterAssignment = np.zeros(Cmeans.shape[0]) * np.nan
clusterAssignment[~allnans] = np.nanargmax(Cmeans[~allnans,:], axis=1)
if bootstrap:
if seed is not None:
np.random.seed(seed)
clusterAssignment_boot = np.zeros((X.shape[0], nrep), dtype=int)
for rep in range(nrep):
print('.', end='', flush=True)
bootgenes = np.random.choice(T.shape[1], T.shape[1], replace=True)
Cmeans_boot = corr2(X[:,bootgenes], means[:,bootgenes])
m = np.zeros(Cmeans.shape[0]) * np.nan
m[~allnans] = np.nanargmax(Cmeans_boot[~allnans,:], axis=1)
clusterAssignment_boot[:,rep] = m
print(' done')
clusterAssignment_matrix = np.zeros((X.shape[0], K))
for cell in range(X.shape[0]):
mapsto, mapsto_counts = np.unique(clusterAssignment_boot[cell,:], return_counts=True)
for i,m in enumerate(mapsto):
clusterAssignment_matrix[cell, m] = mapsto_counts[i] / nrep
if verbose:
for rownum,row in enumerate(clusterAssignment_matrix):
ind = np.argsort(row)[::-1]
ind = ind[:np.where(np.cumsum(row[ind]) >= until)[0][0] + 1]
mystring = []
for i in ind:
s = referenceClusterNames[i] + ' ({:.1f}%)'.format(100*row[i])
mystring.append(s)
mystring = cellNames[rownum] + ': ' + ', '.join(mystring)
print(mystring)
if returnCmeans:
return clusterAssignment, clusterAssignment_matrix, Cmeans
else:
return clusterAssignment, clusterAssignment_matrix
else:
if returnCmeans:
return clusterAssignment, Cmeans
else:
return clusterAssignment