def xcorr(ts1,ts2=None,maxlag=72,freq=12): """ Replicates the matlab function xcorr using rpy2 (which may need to be installed) Input: ts1 and ts2 are timeseries, 1D arrays. If only one array is entered the the auto-correlation will be calculated. maxlag... the maximum lag values freq: For monthly data use freq=12, for annual I guess freq = 1 Output: cor_out: The correlation values at each lag (numpy array) lags: An array with the values of the lags. To match the matlab output and make it easier to plot cross and auto-correlations together, the auto-correlations are 'mirrored' for <0. """ #define R functions rts=robjects.r['ts'] # R function used to create timeseries rccf=robjects.r['ccf'] # R function to calculate cross-correlations racf=robjects.r['acf'] # R function to calculate auto-correlations #Convert python array to an R vector (Floatvector), then an R timeseries ts1_r=rts(robjects.FloatVector(ts1),frequency=freq) if ts2==None: # Use autocorrelation if there's only one timeseries acf_ts1 = racf(ts1_r,lag_max=maxlag,plot=False) ac_ts1=rpyn.ri2numpy(acf_ts1[0])[:,0,0] # Converts R array back to numpy array cor_out=np.concatenate([ac_ts1[::-1],ac_ts1[1:maxlag+1]]) # This mirrors the positive values of the auto-corr elif ts2!=None: ts2_r=rts(robjects.FloatVector(ts2),frequency=freq) ccf_ts12 = rccf(ts1_r,ts2_r,lag_max=maxlag,plot=False) cc_ts12=rpyn.ri2numpy(ccf_ts12[0])[:,0,0] cor_out=cc_ts12 lags=np.concatenate([np.linspace(-maxlag,-1,num=maxlag),np.linspace(0,maxlag,num=maxlag+1)]) return cor_out, lags
def ri2pandas(o):
if isinstance(o, DataFrame):
# use the numpy converter
recarray = numpy2ri.ri2numpy(o)
res = PandasDataFrame.from_records(recarray)
else:
res = ro.default_ri2ro(o)
return res
def getRasterValues(lon, lat, layer, buffervalue):
startTime = time.time()
rinterface.initr()
r = robjects.r
r.require('raster')
ras = r.raster(layer)
rasvalues = r.extract(ras, r.cbind(lon,lat), buffer=buffervalue, small=True)
values = npri.ri2numpy(rasvalues[0])
endTime = time.time()
print(str(endTime - startTime))
return values
def custom_pathways(gene_vals, kegg_file, pval):
importr("KEGGREST")
importr("org.Mm.eg.db")
importr("GSEABase")
result = annotate_ensembl(gene_vals)
sigs = []
univ = []
for key in result:
if float(gene_vals[key]) < float(pval):
sigs.append(result[key])
univ.append(result[key])
ro.globalenv["sigs"] = sigs
ro.globalenv["univ"] = univ
sets = ro.r.getGmt(kegg_file)
ro.globalenv["sets"] = sets
ro.r('genes_pathway <- lapply(sets, geneIds)')
ro.r('names(genes_pathway) <- names(sets)')
ro.r('hyperg <- Category:::.doHyperGInternal')
ro.r('''hyperg_test <- function(pathway_genes, significant_genes, all_genes, over=TRUE) {
white_balls_drawn <- length(intersect(significant_genes, pathway_genes))
white_balls_in_urn <- length(pathway_genes)
total_balls_in_urn <- length(all_genes)
black_balls_in_urn <- total_balls_in_urn - white_balls_in_urn
balls_pulled <- length(significant_genes)
hyperg(white_balls_in_urn, black_balls_in_urn, balls_pulled, white_balls_drawn, over) } ''')
ro.r('pVals_pathway <- t(sapply(genes_pathway, hyperg_test, sigs, univ))')
ro.r('pVals_pathway <- cbind(rownames(pVals_pathway), pVals_pathway)')
pvals = ro.r('pVals_pathway')
vector1=rpyn.ri2numpy(pvals.rx(True,1))
vector2=rpyn.ri2numpy(pvals.rx(True,2))
vector3=rpyn.ri2numpy(pvals.rx(True,3))
vector4=rpyn.ri2numpy(pvals.rx(True,4))
output = open("Hypergeo_pathways.txt", "w")
output.write("Pathway\tP-value\tOddsRatio\tExpected\n"),
for i, j in enumerate(vector1[0]):
output.write("{}\t{}\t{}\t{}\n".format(j, vector2[0][i],vector3[0][i],vector4[0][i])),
output.close()
def manager(request):
params = dict()
params["queries"] = internal.ListQueries(request, {"projectID": [request.session["projectID"]]})
if request.method == "POST":
resp = dict()
queryname = request.POST.get("query", None)
dataset = request.POST.get("dataset", None)
method = request.POST.get("method", None)
category = request.POST.get("category", None)
count = request.POST.get("count", 20)
if not queryname or not dataset or not method or not category:
return HttpResponse(
json.dumps("Please check that the input form is complete."), content_type="application/json"
)
query = Query.objects.get(project=request.session["projectID"], name=queryname)
from rpy2 import robjects
import rpy2.robjects.numpy2ri as rpyn
# fetch Analysis data of interest
heatmapScript = SCRIPTPATH + "r/heatmapDataCreator.R"
robjects.r.source(heatmapScript)
heatmapCommand = robjects.r["heatmapDataCreator"]
profiles1 = Analysis.objects.filter(
project=request.session["projectID"],
dataset=dataset,
method=method,
category=category,
sample__in=query.expandsamples,
).values_list("sample", "entity", "profile")
# format analysis data and load into R
profiles = zip(*profiles1)
profileRdata = robjects.DataFrame(
{
"samples": robjects.StrVector(profiles[0]),
"entity": robjects.StrVector(profiles[1]),
"profile": robjects.FloatVector(profiles[2]),
}
)
processedMatrix = heatmapCommand(profileRdata, count)
vector = rpyn.ri2numpy(processedMatrix)
resp["rows"] = list(processedMatrix.rownames)
resp["cols"] = list(processedMatrix.colnames)
resp["maxVal"] = numpy.amax(vector)
resp["minVal"] = numpy.amin(vector)
resp["data"] = vector.tolist()
return HttpResponse(json.dumps(resp), content_type="application/json")
return render(request, "heatmap.html", params)
def from_dtw2dict(alignment):
"""Auxiliar function which transform useful information of the dtw function
applied in R using rpy2 to python formats.
"""
dtw_keys = list(alignment.names)
bool_traceback = 'index1' in dtw_keys and 'index2' in dtw_keys
bool_traceback = bool_traceback and 'stepsTaken' in dtw_keys
## Creating a dict to save all the information in python format
dtw_dict = {}
# Transformation into a dict
dtw_dict['stepPattern'] = ri2numpy(alignment.rx('stepPattern'))
dtw_dict['N'] = alignment.rx('N')[0]
dtw_dict['M'] = alignment.rx('M')[0]
dtw_dict['call'] = alignment.rx('call')
dtw_dict['openEnd'] = alignment.rx('openEnd')[0]
dtw_dict['openBegin'] = alignment.rx('openBegin')[0]
dtw_dict['windowFunction'] = alignment.rx('windowFunction')
dtw_dict['jmin'] = alignment.rx('jmin')[0]
dtw_dict['distance'] = alignment.rx('distance')[0]
dtw_dict['normalizedDistance'] = alignment.rx('normalizedDistance')[0]
if bool_traceback:
aux = np.array(ri2numpy(alignment.rx('index1')).astype(int))
dtw_dict['index1'] = aux
aux = np.array(ri2numpy(alignment.rx('index2')).astype(int))
dtw_dict['index2'] = aux
dtw_dict['stepsTaken'] = ri2numpy(alignment.rx('stepsTaken'))
elif 'localCostMatrix' in dtw_keys:
aux = np.array(ri2numpy(alignment.rx('localCostMatrix')))
dtw_dict['localCostMatrix'] = aux
elif 'reference' in dtw_keys and 'query' in dtw_keys:
dtw_dict['reference'] = alignment.rx('reference')
dtw_dict['query'] = alignment.rx('query')
return dtw_dict
def matrix_to_normcount(matrix, samples):
# read normalized count from matrix (row=clone; col=sample) and
# update the samples' clones
samplenames = matrix.colnames
cloneids = matrix.rownames
for sample in samples:
if sample.name not in samplenames:
sys.stderr.write(("Warning: sample %s does not have normalized "
% sample.name + "count."))
continue
for clone in sample.clones:
normcount = 0.0
for id in clone.vjseq_ids:
assert id in cloneids
nc = matrix.rx[id, sample.name]
normcount = normcount + rpyn.ri2numpy(nc)[0]
clone.set_normcount(normcount)
return samples
w0 = [1, 0.75, 0.75, 0.5, 0.5, 0.5, 0.25, 0.25, 0.25, 0.25, 0, 0, 0, 0, 0]
w1 = [0, 0.25, 0, 0.5, 0.25, 0, 0.75, 0.5, 0.25, 0, 1, 0.75, 0.5, 0.25, 0]
w2 = [0, 0, 0.25, 0, 0.25, 0.5, 0, 0.25, 0.5, 0.75, 0, 0.25, 0.5, 0.75, 1]
path = './matrix_dist_norm/'
files = getfiles(path)
subset0 = []
subset1 = []
subset2 = []
print "Subset 0"
for index, file in enumerate(files[:3]):
sub = 0
m = r("readRDS('"+ str(file)+"')")
mat = rpyn.ri2numpy(m)
subset0.append(mat)
print "Calculating..."
calculate(subset0, w0, w1, w2, sub)
print "end\n"
print "Subset 1"
for index, file in enumerate(files[3:6]):
sub = 1
m = r("readRDS('"+ str(file)+"')")
mat = rpyn.ri2numpy(m)
subset1.append(mat)
print "Calculating..."
calculate(subset1, w0, w1, w2, sub)
# some simple R things
print R.r.median(R.IntVector([1,2,3,4]))[0]
# create two R vectors and do correlation coefficient in R
a = R.IntVector([1,2,3,4])
b = R.IntVector([1,2,3,4])
# need the subscript to get authentic python type?
print R.r.cor(a,b,method="pearson")[0]
my_vec = R.IntVector([1,2,3,4])
my_chr_vec = R.StrVector(['aaa','bbb'])
my_float_vec = R.FloatVector([0.001,0.0002,0.003,0.4])
print "\nconvert to numpy array?"
vector = rpyn.ri2numpy(my_float_vec)
print vector
python_list = list(my_float_vec)
print python_list
bigger_vec = R.IntVector(a+b) # using multiple lists
print list(bigger_vec)
# linear regression
observed = R.FloatVector([1.1, 1.2, 1.3]) # native python list will not do!!
theoretical = R.FloatVector([1.15, 1.25, 1.35])
R.globalEnv['observed'] = observed
R.globalEnv['theoretical'] = theoretical
m = R.r.lm('theoretical ~ observed')
def rx(data, var):
return rpyn.ri2numpy(data.rx2(var))
import numpy as np
import rpy2.robjects as ro
import rpy2.robjects.numpy2ri as n2r
n2r.activate()
r = ro.r
r.library('glmnet')
# input files (for this example) need to have header and NO index column
X = np.loadtxt('./x.csv', dtype=float, delimiter=',', skiprows=1)
y = np.loadtxt('./y.csv', dtype=int, delimiter=',', skiprows=1)
y = ro.FactorVector(list(y.transpose())) # use factors
trained_model = r['cv.glmnet'](X, y, nfolds=3, family="binomial")
lambda_ = np.asanyarray(trained_model.rx2('lambda'))
cvm_ = np.asanyarray(trained_model.rx2('cvm'))
cvsd_ = np.asanyarray(trained_model.rx2('cvsd'))
lambda_min = np.asanyarray(trained_model.rx2('lambda.min'))[0]
min_cvm = cvm_[np.argwhere(lambda_ == lambda_min)[0][0]]
idx = np.argwhere(cvm_ < min_cvm + 0.1 * cvsd_)
idx[0]
fit = trained_model.rx2('glmnet.fit')
beta = n2r.ri2numpy(r['as.matrix'](fit.rx2('beta')))
relvars = np.argwhere(beta[:, idx[0]].transpose()[0] > 1e-5)
print relvars.transpose()[0]
def testAtomicVectorToNumpy(self):
v = robjects.vectors.IntVector((1,2,3))
a = rpyn.ri2numpy(v)
self.assertTrue(isinstance(a, numpy.ndarray))
self.assertEqual(1, v[0])
def testDataFrameToNumpy(self):
df = robjects.vectors.DataFrame(dict((('a', 1), ('b', 2))))
reca = rpyn.ri2numpy(df)
self.assertTrue(isinstance(reca, numpy.recarray))
self.assertEqual(1, reca.a[0])
self.assertEqual(2, reca.b[0])
def fa(source=False, use_filter="default", data_file="latest", participant_subset="", drop_metadata=True, drop=[], clean=7, factors=5, facecolor="#ffffff"):
#gets config file:
config = get_config_file(localpath=path.dirname(path.realpath(__file__))+'/')
#IMPORT VARIABLES
if not source:
source = config.get('Source', 'source')
data_path = config.get('Addresses', source)
filter_dir = config.get('Paths', "filter_dir")
filter_name = config.get("Filters", use_filter)
#END IMPORT VARIABLES
filter_path = path.dirname(path.realpath(__file__)) + '/' + filter_dir + filter_name + '.csv'
filters = DataFrame.from_csv(filter_path, header=None).transpose() # transpose filters because of .csv file formatting
all_data = DataFrame.from_csv(data_path + data_file + ".csv")
all_data = all_data.reset_index(level=0)
#~ print filters["metadata"]
#clean data of respondents who only ckeck extreme answers:
all_data = all_data[map(lambda y: len(set(y)) > clean,np.array(all_data))]
if drop_metadata == True:
# drops metadata
all_data = all_data.drop(filters["metadata"][Series.notnull(filters["metadata"])], axis=1)
drop_list = []
for drop_item in drop:
# compile list of column names to be dropped:
drop_list += list(filters[drop_item][Series.notnull(filters[drop_item])])
#get unique column names (the list may contain duplicates if overlaying multiple filters):
drop_list = list(set(drop_list))
all_data = all_data.drop(drop_list, axis=1)
if participant_subset == "odd":
# selects only odd indexes (keep the other dataset half for validation)
keep_rows = all_data.index.values[1::2]
filtered_data = all_data.ix[keep_rows]
elif participant_subset == "even":
# selects only even indexes (keep the other dataset half for validation)
keep_rows = all_data.index.values[0::2]
filtered_data = all_data.ix[keep_rows]
elif participant_subset == "male":
# selects only male participants
filtered_data = all_data[all_data['My legal gender:'] == 'Male']
elif participant_subset == "female":
# selects only female participants
filtered_data = all_data[all_data['My legal gender:'] == 'Female']
else:
filtered_data = all_data
#convert to correct type for analysis:
filtered_data_array = np.array(filtered_data, dtype='float64')
filtered_data_array = filtered_data_array / 100
fit = r.factanal(filtered_data_array, factors, rotation='promax')
load = r.loadings(fit)
load = numpy2ri.ri2numpy(load)
load = r.t(load)
remapped_cmap = remappedColorMap(cm.PiYG, start=(np.max(load)-abs(np.min(load)))/(2*np.max(load)), midpoint=abs(np.min(load))/(np.max(load)+abs(np.min(load))), name='shrunk')
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(17.5, 5), facecolor=facecolor)
graphic = ax.imshow(load, cmap = remapped_cmap, interpolation='none')
ax.xaxis.set_major_locator(matplotlib.ticker.MultipleLocator(base=1.0))
ax.yaxis.set_major_locator(matplotlib.ticker.MultipleLocator(base=1.0))
ax.set_xticklabels([0]+filtered_data.columns.tolist(),fontsize=8,rotation=90)
ax.set_yticklabels(np.arange(factors+1))
ax.set_ylabel('Factors')
ax.set_title("Question Loadings on Factors")
#Recolor plot spines:
for spine_side in ["bottom", "top", "left", "right"]:
ax.spines[spine_side].set_color("#777777")
#Remove ticks:
plt.tick_params(axis='both', which='both', left="off", right="off", bottom='off', top='off')
divider = make_axes_locatable(ax)
#calculate width for cbar so that it is equal to the question column width:
cbar_width = str(100/np.shape(load)[1])+ "%"
cax = divider.append_axes("right", size=cbar_width, pad=0.05)
cbar = colorbar(graphic, cax=cax, drawedges=True)
#Limit the number of ticks:
tick_locator = ticker.MaxNLocator(nbins=6)
cbar.locator = tick_locator
cbar.update_ticks()
#Align ticklabels so that negative values are not misaligned (meaning right align):
for t in cbar.ax.get_yticklabels():
t.set_horizontalalignment('right')
t.set_x(0.045*(np.shape(load)[1]+6))
#Tweak color bar borders
cbar.outline.set_color("#666666")
cbar.dividers.set_linewidth(0)
def testAtomicVectorToNumpy(self):
v = robjects.vectors.IntVector((1, 2, 3))
a = rpyn.ri2numpy(v)
self.assertTrue(isinstance(a, numpy.ndarray))
self.assertEqual(1, v[0])
def doMigration(self, ipSrc, movUsers, ipDst, dstUsers):
cacheSize = self.getCacheSize(ipDst[0], ipSrc[0][0])
dIntSrc = []
for src in range(len(ipSrc)):
dIntSrc.append(self.getMergedInterests(ipSrc[src], "1 months"))
dIntDst = self.getMergedInterests(ipDst, "1 months")
#Aux Lists
auxB = []
auxC = []
auxL = []
auxS = []
numCells = len(dIntSrc) + 1
# need mapping (-1)
cnt = 1
print "Processing 1st Source Interests"
# Adding prefixes requested at 1st source
for k,v in dIntSrc[0].items():
popDst = dIntDst[k][1] if k in dIntDst else 0
popSrcs = 0
for i in range(numCells-1):
popSrcs += (dIntSrc[i][k][1] if k in dIntSrc[i] else 0) * movUsers[i]
popInt = (popSrcs + popDst*dstUsers) / numCells
### ID | Populatiry
auxB.extend([cnt, popInt])
### ID | File Size
auxC.extend([cnt, v[0]])
auxL.append(k)
auxS.append(v[0])
cnt += 1
print "Processing other Sources Interests"
for j in range(1,numCells-1):
for k,v in dIntSrc[j].items():
if k not in auxL:
popSrcs += (dIntSrc[i][k][1] if k in dIntSrc[i] else 0) * movUsers[i]
popSrcs = 0
for i in range(j, numCells-1):
popSrcs += (dIntSrc[i][k][1] if k in dIntSrc[i] else 0) * movUsers[i]
popInt = (popSrcs + popDst*dstUsers) / numCells
### ID | Populatiry
auxB.extend([cnt, popInt])
### ID | File Size
auxC.extend([cnt, v[0]])
auxL.append(k)
auxS.append(v[0])
cnt += 1
print "Processing Destination Interests"
# Adding interests requested at destination still missing
for k,v in dIntDst.items():
if k not in auxL:
popInt = (v[1]*dstUsers) / numCells
### ID | Populatiry
auxB.extend([cnt, popInt])
### ID | File Size
auxC.extend([cnt, v[0]])
auxL.append(k)
auxS.append(v[0])
cnt += 1
print "Going to run MADM"
## Create matrix Ben and matrix Cost
mBen = r.matrix(auxB, ncol=2, byrow=True)
mCost = r.matrix(auxC, ncol=2, byrow=True)
vBen = ro.FloatVector([1.0])
vCost = ro.FloatVector([1.0])
output = MADM(mBen,mCost,vBen,vCost,1)
if output == -1:
return 200
#print output
outAux = rpyn.ri2numpy(output)
if outAux[0] == -2:
return 200
elif outAux[0] == -1:
code = self.sendMigrationData(auxL, ipDst)
return code
cacheList = []
usedCache = 0
for out in outAux:
if auxS[int(out[0])-1] + usedCache < cacheSize:
cacheList.append(auxL[int(out[0]-1)])
usedCache += auxS[int(out[0]-1)]
if usedCache == cacheSize:
break
#for ent in cacheList:
#print ent
code = self.sendMigrationData(cacheList, ipDst)
return code
# some simple R things
print R.r.median(R.IntVector([1, 2, 3, 4]))[0]
# create two R vectors and do correlation coefficient in R
a = R.IntVector([1, 2, 3, 4])
b = R.IntVector([1, 2, 3, 4])
# need the subscript to get authentic python type?
print R.r.cor(a, b, method="pearson")[0]
my_vec = R.IntVector([1, 2, 3, 4])
my_chr_vec = R.StrVector(['aaa', 'bbb'])
my_float_vec = R.FloatVector([0.001, 0.0002, 0.003, 0.4])
print "\nconvert to numpy array?"
vector = rpyn.ri2numpy(my_float_vec)
print vector
python_list = list(my_float_vec)
print python_list
bigger_vec = R.IntVector(a + b) # using multiple lists
print list(bigger_vec)
# linear regression
observed = R.FloatVector([1.1, 1.2, 1.3]) # native python list will not do!!
theoretical = R.FloatVector([1.15, 1.25, 1.35])
R.globalenv['observed'] = observed
R.globalenv['theoretical'] = theoretical
m = R.r.lm('theoretical ~ observed')
# R.abline(lm,col='color') # add regression line to EXISTING plot
# Transform URL string into normal string in python (%20 to space etc) rpy2: Convert FloatVector or Matrix back to a Python array or list? import rpy2.robjects.numpy2ri as rpyn vector=rpyn.ri2numpy(vector_R)
parfOrig_r = IntVector(parfOrig)
parfOrig_rc = r.circular(parfOrig_r, units='degrees', template='geographics')
# optimal bandwith determined based on a VonMises distribution
# using circular.bw_nrd_circular()
if reg == 'andes':
bandwith = 2.0
elif reg == 'qf':
bandwith = 3.5
elif reg == 'amazon':
bandwith = 1.0
# calculate circular density
print 'calculating density for ' + paramOrig + ', please wait...'
dens = r.density(parfOrig_rc, bw=bandwith, kernel='vonmises')
print 'density for ' + paramOrig + ' OK'
# get density values back to python
densX = rpyn.ri2numpy(dens[1])
densY = rpyn.ri2numpy(dens[2])
gc.collect()
# densityOrig = ss.kde.gaussian_kde(parfOrig)
# x = np.arange(0., np.max(parfOrig), .1)
# yOrig = densityOrig(x)
# plot
# cartesian plot
fig = reg + '_aspect_compass_original_density_circular.svg'
print 'fig will be: ' + fig
plt.ylabel('density')
plt.xlabel('aspect_compass')
plt.plot(densX, densY, label=paramOrig)
plt.xticks((-270, -180, -90, 0, 90), ('E','S','W','N','E'))
print 'cartesian plot for ' + paramOrig + ' OK'
gc.collect()
def testDataFrameToNumpy(self):
df = robjects.vectors.DataFrame(dict((('a', 1), ('b', 2))))
reca = rpyn.ri2numpy(df)
self.assertTrue(isinstance(reca, numpy.recarray))
self.assertEqual(1, reca.a[0])
self.assertEqual(2, reca.b[0])
