def _plot(self, x_list, y_list, x_range, y_range): self.no_of_curves += 1 if self.no_of_curves==1: r.plot(x_list, y_list, type='o',pch='*',xlab='dataset no.',xlim=x_range,ylim=y_range, \ ylab='expression value', col=self.no_of_curves) else: r.lines(x_list, y_list, type='o',pch='*',col=self.no_of_curves)
def plotSk(self, xlab='', ylab='', type='l', col=1, ylim=(0, 15),
**other):
from rpy import r
r.plot(self.kmags(), self.SkAverages(),
xlab=xlab, ylab=ylab, type=type, col=col,
ylim=ylim, **other
)
def funcion(dato,opciones):
from rpy import r
diccionario={}
if opciones.has_key("Cuantiles"):
if opciones["Cuantiles"][u"DirecciónCola"]=='izquierda':
sentido=True
else:
sentido=False
diccionario["cuantiles"]=r.qnorm([float(opciones["Cuantiles"]["Probabilidad"])],mean=float(opciones["Cuantiles"]["Media"]),sd=float(opciones["Cuantiles"][u"Desviación"]),lower_tail=sentido)
if opciones.has_key("Probabilidades"):
if opciones["Probabilidades"][u"DirecciónCola"]=='izquierda':
sentido=True
else:
sentido=False
diccionario["probabilidades"]=r.pnorm([float(opciones["Probabilidades"]["Valores"])],mean=float(opciones["Probabilidades"]["Media"]),sd=float(opciones["Probabilidades"][u"Desviación"]),lower_tail=sentido)
if opciones.has_key(u"Gráfica"):
import random
nombrefichero="/tmp/driza"+str(random.randint(1,99999))+".png"
diccionario["ruta"]=nombrefichero
r.png(nombrefichero) #Directorio temporal de la config
lista=r.seq(-3.291, 3.291, length=100)
if opciones[u"Gráfica"]["Tipografica"]=="Densidad":
etiquetay="Densidad"
mifuncion=r.dnorm
else:
etiquetay="Probabilidad acumulada"
mifuncion=r.pnorm
r.plot(lista, mifuncion(lista, mean=float(opciones[u"Gráfica"]["Media"]), sd=float(opciones[u"Gráfica"][u"Desviación"])), xlab="x", ylab=etiquetay, main=r.expression(r.paste("Normal Distribution: ", "mu", " = 0, ", "sigma", " = 1")), type="l")
r.abline(h=0, col="gray")
r.dev_off()
return diccionario
def scatter_plot(self, gene_id_list, output_fname='/tmp/scatter_plot.ps'):
"""
02-15-06
1st gene is regarded as X, all others genes are treated as Y
"""
vector_list = []
#gene_id_list may contain some inexistent genes
real_gene_id_list = []
for gene_id in gene_id_list:
if gene_id in self.gene_id2expr_array:
real_gene_id_list.append(gene_id)
vector_list.append(self.gene_id2expr_array[gene_id])
else:
sys.stderr.write("%s doesn't appear in the dataset\n"%(gene_id))
if len(real_gene_id_list)>0:
r.postscript("%s"%output_fname)
axis_range = self.get_min_max(vector_list)
no_of_curves = 1 #counting starts from 1st gene itself.
no_of_curves += 1
r.plot(vector_list[0], vector_list[1], xlab='value of %s'%real_gene_id_list[0], xlim=axis_range, ylim=axis_range, \
ylab='other genes values', col=no_of_curves)
for i in range(2, len(vector_list)):
no_of_curves += 1
r.points(vector_list[0], vector_list[i], col=no_of_curves)
r.legend(axis_range[1], axis_range[1], gene_id_list, col=range(1, no_of_curves+1), lty=1, xjust=1)
r.dev_off()
return output_fname
else:
return None
def drawCpuUsage(d,xat,xlbs,pic):
data=r.c(d)
pch = 22 # point like like a square
lty = 1 # line style solid line
col = "blue" # line color
ltype = "o" # line only http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html
ylim = (0,100) # y domain
xaxis=1
yaxis=2
vertical_text=2
horizontal_text=1
text_size=0.8
yat=[x for x in range(0,110,10)]
ylbs=["%d%%"%x for x in yat]
legend_x=1
legend_y=100
# for r.text method
warn_val=40 # val over this value will display a text on point
xtext=[idx for idx,val in enumerate(d) if val > warn_val] # text x pos
ytext=[val for idx,val in enumerate(d) if val > warn_val] # text y pos
labtext=["%d%%"%val for idx,val in enumerate(d) if val > warn_val] # label for text
# summary
dmax=max(d)
sumry="max %.2f%%" % dmax
sumrycol="red" if dmax>50 else "green"
# plot
r.png(pic, width=900,height=450*0.6)
r.plot(data, type=ltype, col=col, ylim=ylim, pch=pch, lty=lty, axes=False, ann=False)
# draw text that over 40
# http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/text.html
r.text(xtext, ytext, labels=labtext, pos=3, cex=0.8, col="red")
# summary text
r.mtext(sumry, side=3, cex=1, col=sumrycol)
# axis
r.axis(xaxis, las=vertical_text, at=xat, lab=r.c(xlbs))
r.axis(yaxis, las=horizontal_text, at=yat, lab=r.c(ylbs))
r.box()
# titles
r.title(main="CPU Sampling")
r.title(xlab="Time")
r.title(ylab="CPU Usage")
# reference line
# r.abline(h=50, col="gray") # at 50%
# legend
r.legend(legend_x, legend_y, r.c(("trunk")), col=col, cex=text_size, pch=pch, lty=lty)
r.dev_off()
def main():
in_fname = sys.argv[1]
out_fname = sys.argv[2]
try:
columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
except:
stop_err( "Columns not specified, your query does not contain a column of numerical data." )
title = sys.argv[5]
xlab = sys.argv[6]
ylab = sys.argv[7]
matrix = []
skipped_lines = 0
first_invalid_line = 0
invalid_value = ''
invalid_column = 0
i = 0
for i, line in enumerate( file( in_fname ) ):
valid = True
line = line.rstrip( '\r\n' )
if line and not line.startswith( '#' ):
row = []
fields = line.split( "\t" )
for column in columns:
try:
val = fields[column]
if val.lower() == "na":
row.append( float( "nan" ) )
else:
row.append( float( fields[column] ) )
except:
valid = False
skipped_lines += 1
if not first_invalid_line:
first_invalid_line = i + 1
try:
invalid_value = fields[column]
except:
invalid_value = ''
invalid_column = column + 1
break
else:
valid = False
skipped_lines += 1
if not first_invalid_line:
first_invalid_line = i + 1
if valid:
matrix.append( row )
if skipped_lines < i:
try:
r.pdf( out_fname, 8, 8 )
r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
r.dev_off()
except Exception, exc:
stop_err( "%s" % str( exc ) )
def qqplot_density(samples, density_x, density_y):
from rpy import r
# LAME: should do better quantile calculation. r.quantile() returns a
# hard-to-use dictionary unfortunately. r.approx() as per ?quantile, maybe.
percs = list(np.arange(1,100, .1))
data_perc=np.percentile(samples, percs)
real_perc=np.percentile(r.sample(density_x, len(samples)*10, prob=density_y, replace=True), percs)
r.plot(real_perc, data_perc, xlab='',ylab='',main='');
r.abline(a=0,b=1,col='blue')
def plot(self, outputfname, fix_index_ls, parameter_list, var_index, variant_ls, parameter_index2label, y_axis_ls, y_label):
outputfname = '%s_%s2%s.png'%(outputfname, y_label, parameter_index2label[var_index])
sys.stderr.write('Plotting %s'%outputfname)
r.png(outputfname)
r.plot(variant_ls, y_axis_ls, main='%s vs %s (%s=%s, %s=%s)'%(y_label, parameter_index2label[var_index],\
parameter_index2label[fix_index_ls[0]], parameter_list[fix_index_ls[0]], parameter_index2label[fix_index_ls[1]],\
parameter_list[fix_index_ls[1]]), xlab=parameter_index2label[var_index], ylab=y_label)
r.dev_off()
sys.stderr.write('Done.\n')
def hist_plot(self, dict, filename, xlabel, ylabel):
#convert self.go_no2cluster and self.go_no2gene into histograms
r.png('%s'%filename)
x_list = []
y_list = []
for (key, value) in dict.iteritems():
x_list.append(key)
y_list.append(len(value))
r.plot(x_list, y_list, type='h', xlab=xlabel, ylab=ylabel, main='%s v.s. %s'%(ylabel, xlabel))
r.dev_off()
def trace_plots(history, burnin):
from rpy import r
h = np.array(history)
print "{} total, {} burning, {} remaining".format(len(history), burnin, len(history)-burnin)
r.par(mfrow=[2,2])
r.acf(h[burnin:])
r.plot(h,xlab='',ylab='',main='')
r.abline(v=burnin, col='blue')
#r.hist(h[burnin:],breaks=30,xlab='',ylab='',main='histogram')
r.plot(r.density(h[burnin:]), xlab='',ylab='',main='density')
def qqplot_density(samples, density_x, density_y):
from rpy import r
# LAME: should do better quantile calculation. r.quantile() returns a
# hard-to-use dictionary unfortunately. r.approx() as per ?quantile, maybe.
percs = list(np.arange(1, 100, .1))
data_perc = np.percentile(samples, percs)
real_perc = np.percentile(
r.sample(density_x, len(samples) * 10, prob=density_y, replace=True),
percs)
r.plot(real_perc, data_perc, xlab='', ylab='', main='')
r.abline(a=0, b=1, col='blue')
def plot_binning(entries, main=None):
for entry in entries:
number, fullname, tarray = entry
if main==None:
this_main = fullname
else:
this_main = main
if len(tarray)>0:
r.plot(range(len(tarray)), tarray, xlab="bin index", ylab="center value", main=this_main)
def trace_plots(history, burnin):
from rpy import r
h = np.array(history)
print "{} total, {} burning, {} remaining".format(len(history), burnin,
len(history) - burnin)
r.par(mfrow=[2, 2])
r.acf(h[burnin:])
r.plot(h, xlab='', ylab='', main='')
r.abline(v=burnin, col='blue')
#r.hist(h[burnin:],breaks=30,xlab='',ylab='',main='histogram')
r.plot(r.density(h[burnin:]), xlab='', ylab='', main='density')
def plots(regression_o, getData_o):
"""Plots the dataset with a regression line and a boxplot using R."""
fname1 = 'car_regress.pdf'
r.pdf(fname1)
r.plot(getData_o, ylab='dist', xlab='speed')
r.abline(regression_o['(Intercept)'], regression_o['y'], col='red')
r.dev_off()
fname2 = 'car_hist.pdf'
r.pdf(fname2)
r.boxplot(getData_o, names=['dist', 'speed'])
r.dev_off()
return fname1, fname2
def hist_plot_ratio(self, dict1, dict2, filename, xlabel, ylabel):
#convert self.go_no2cluster and self.go_no2gene into histograms
r.png('%s'%filename)
x_list = []
y_list = []
keys = Set(dict1.keys()).union( Set(dict2.keys()) )
for key in keys:
value1 = dict1.get(key, [])
value2 = dict2.get(key, [])
ratio = float(len(value1))/(len(value1)+len(value2))
x_list.append(key)
y_list.append(ratio)
r.plot(x_list, y_list, type='h', xlab=xlabel, ylab=ylabel, main='%s v.s. %s'%(ylabel, xlabel))
r.dev_off()
def output(self):
self.matrix = array(self.result_array)
p_value_list = map(str, self.p_value_list)
self.of.write('p_value\t%s\n'%'\t'.join(p_value_list))
df = self.df_lower
for cor_list in self.result_array:
cor_list = map(str, cor_list) #string can be 'join'ed. easy to output
self.of.write('%d\t%s\n'%(df, '\t'.join(cor_list)))
df += 1
r.pdf('p_value_cor.pdf')
#select a column to plot
cor_list = self.matrix[:,self.column]
p_value_label = self.p_value_list[self.column]
df_list = range(self.df_lower, self.df_upper+1)
r.plot(df_list, cor_list, type='o', pch='*', xlab='df', ylab='correlation', main='p_value: %s'%p_value_label)
r.dev_off()
def test():
data=r.c([1.25,3.45,6.75,20.2,9.9])
# draw image using rpy
r.png("test.png", width=300,height=300)
r.plot(data, type="o", col="blue", ylim=(0,100), pch=22, lty=1, axes=False, ann=False)
r.axis(1, at=(1,2,3,4,5), lab=r.c("a","b","c","d","e"))
r.axis(2, las=1, at=(0,50,100))
r.box()
r.title(main="CPU usage sampling result")
r.title(xlab="Time")
r.title(ylab="CPU")
r.legend(1,100,r.c("trunk"), cex=0.8, col=r.c("blue"), pch=22, lty=1)
r.dev_off()
def plot(self):
vertex_list = self.graph.node_list()
number_of_nodes = len(vertex_list)
for vertex in vertex_list:
degree = self.graph.inc_degree(vertex) + self.graph.out_degree(vertex)
if degree not in self.degree_dict:
self.degree_dict[degree] = 1
else:
self.degree_dict[degree] += 1
r.pdf('degree_distribution.pdf')
x_list = []
y_list = []
for degree in self.degree_dict:
x_list.append(r.log(degree))
y_list.append(r.log(float(self.degree_dict[degree])/number_of_nodes))
r.plot(x_list, y_list, type='p', xlab='log(k)', ylab='log(p(k))')
r.dev_off()
def plot_bin_widths(entries, log_space=False, main=None):
for entry in entries:
number, fullname, tarray = entry
if log_space:
tarray = numpy.log(tarray)
ylab = r("expression(ln(Delta[bin]))")
else:
ylab = r("expression(Delta[bin])")
if main==None:
this_main = fullname
else:
this_main = main
if len(tarray)>0:
r.plot(range(len(tarray)), tarray, xlab="bin number", ylab=ylab, main=this_main)
def __print_entropies(self, entropies):
"""
This is for debugging purposes.
"""
try:
from rpy import r
except:
print "Could not import rpy module"
return
r.postscript(DEBUG_ENTROPIES_FILE)
r.plot(entropies, type='b', xlab="Iterations", ylab="Entropy")
r.dev_off()
return
def plotLabelLegend(self, colVecL, labelPhenoD, filename=None, legendDir=None, type='png'):
if filename is None:
filename = 'legend_label_%i' % len(labelPhenoD.keys())
if legendDir is None:
legendDir = self.legendDir
full_filename = os.path.join(legendDir, filename)
labelL = labelPhenoD.keys()
labelL.sort()
phenoL = [labelPhenoD[x] for x in labelL]
rdev = plot_utilities.RDevice(name = full_filename, title='', plotType=type,
width=300, height=200)
r("par(mar=c(0,0,0,0))")
r.plot([1, 2, 3], type="n", xlab="", ylab="", main="", ann=False, axes=False)
r.legend(x="center", legend = phenoL, fill=colVecL, bg = "white", bty="n", cex=0.7)
rdev.close()
def _plot(self, row):
self.no_of_curves += 1
#position 3 in row is the varying value
self.varying_list.append(row[3])
x_list = []
y_list = []
self.curs.execute("select tp, tp_m, tp1, tp1_m, tn, fp, fp_m, fn from stat_plot_data where\
%s=%s and %s=%s and %s=%s and %s=%s and tag='%s' order by p_value_cut_off"%\
(self.option_num_dict[0].label, row[0], self.option_num_dict[1].label, row[1], self.option_num_dict[2].label,\
row[2], self.option_num_dict[3].label, row[3], row[4]))
plot_data = self.curs.fetchall()
for entry in plot_data:
tn = entry[4]
fn = entry[7]
if self.based_on_clusters:
#using the tp_m, tp1_m and fp_m
tp = entry[1]
tp1 = entry[3]
fp = entry[6]
else:
#using the tp, tp1, fp
tp = entry[0]
tp1 = entry[2]
fp = entry[5]
if self.l1:
#tp1 is counted as true positive
tp += tp1
else:
#tp1 is counted as false positive
fp += tp1
x_list.append(tp)
y_list.append(float(tp)/(tp+fp))
if self.no_of_curves==1:
r.plot(x_list, y_list, type='o',pch='*',xlab='consistent predictions',xlim=self.x_range,ylim=self.y_range, \
ylab='percentage', main='%s'%(self.option_num_dict[3].label), col=self.no_of_curves)
else:
r.lines(x_list, y_list, type='o',pch='*',col=self.no_of_curves)
def __init__(self, bedfile, dir, win, ma, out, ymin=0, ymax=0):
self.L = 17 # number of letters per line
Bed.__init__(self, bedfile)
self.dir = dir
self.win = win + ma
self.ma = ma # window for moving average
try:
from rpy import r
r.pdf(out + '.ConservationPlot.pdf')
self.Run()
if not ymin:
ymin = self.mscore[self.mscore > 0].min() - 0.05
if not ymax:
ymax = self.mscore.max() + 0.05
r.plot(range(-1*win, win+1), self.mscore, type = 'l', xlab = \
'Distance from the Center of Enriched Regions', \
ylab = 'Conservation Score', lwd= 3, ylim = (ymin, ymax))
r.dev_off()
except:
print >> sys.stderr, 'error import r using rpy, will not generate phastCons plot'
print sys.exc_info()[0], sys.exc_info()[1]
def single_plot(self):
#this function deals with 4 fixed parameters and 1 varying parameter
r.png('%s'%self.ofname)
x_list = []
y_list = []
self.curs.execute("select tp, tp_m, tp1, tp1_m, tn, fp, fp_m, fn from\
stat_plot_data where %s=%s and %s=%s and %s=%s and %s=%s and tag='%s' order by %s \
"%(self.option_num_dict[0].label, self.option_num_dict[0].value, \
self.option_num_dict[1].label, self.option_num_dict[1].value, self.option_num_dict[2].label, \
self.option_num_dict[2].value, self.option_num_dict[3].label, self.option_num_dict[3].value, \
self.tag, self.option_num_dict[4].label))
plot_data = self.curs.fetchall()
for entry in plot_data:
tn = entry[4]
fn = entry[7]
if self.based_on_clusters:
#using the tp_m, tp1_m and fp_m
tp = entry[1]
tp1 = entry[3]
fp = entry[6]
else:
#using the tp, tp1, fp
tp = entry[0]
tp1 = entry[2]
fp = entry[5]
if self.l1:
#tp1 is counted as true positive
tp += tp1
else:
#tp1 is counted as false positive
fp += tp1
x_list.append(tp)
y_list.append(float(tp)/(tp+fp))
r.plot(x_list, y_list, type='o',pch='*',xlab='consistent predictions',xlim=self.x_range,ylim=self.y_range, \
ylab='percentage', main='%s'%(self.option_num_dict[4].label), col=1)
r.dev_off()
def plot(self):
r.pdf("per_p_value05.pdf")
r.plot(self.dataset_no, self.per_05, type='o', pch='*', xlab='dataset no.',\
ylab='percentage', main='p_value: 0.05. #edges compared with correlation cut_off 0.6')
r.dev_off()
r.pdf("per_p_value025.pdf")
r.plot(self.dataset_no, self.per_025, type='o', pch='*', xlab='dataset no.',\
ylab='percentage', main='p_value: 0.025. #edges compared with correlation cut_off 0.6')
r.dev_off()
r.pdf("per_p_value01.pdf")
r.plot(self.dataset_no, self.per_01, type='o', pch='*', xlab='dataset no.',\
ylab='percentage', main='p_value: 0.01. #edges compared with correlation cut_off 0.6')
r.dev_off()
def generateCountsGraph(self, counts, sitename, widthpx=648, resol=72, ):
'''
Static function to generate graph file via R.
Graphs *all* of the counts records contained in counts List
'''
from rpy import r as robj
# Calculate graph image information
widthpx = int(widthpx)
imgwidth = int( float(widthpx) / float(resol) )
ratio = float(self.config.get('data','graphratio'))
imgheight = int( (float(widthpx) * ratio) / float(resol) ),
counts_data = {"datetime":[],
"c1":[]}
(fd, tmpgraphfile)= mkstemp()
logobject.debug("DataHandler.generateCountsGraph(): Temp graph filename = %s" % tmpgraphfile)
for cr in counts:
#logobject.debug("%s" % c)
epochsecs = time.mktime(cr.datetime.timetuple())
counts_data["datetime"].append( epochsecs )
#counts_data["datetime"].append( "%s" % c.datetime )
#logobject.debug("Datetime %s converted to epoch %d" % (c.datetime, epochsecs ))
counts_data["c1"].append(cr.c1)
cts = counts_data['c1']
ctm = counts_data['datetime']
if len(cts) > 0:
robj.bitmap(tmpgraphfile,
type = "png256",
width = imgwidth ,
height = imgheight,
res = resol,
)
ymin = int(self.config.get('data','counts.graph.ylim.min'))
ymax = int(self.config.get('data','counts.graph.ylim.max'))
robj.plot(ctm, cts,
col="black",
main="Counts: %s" % sitename ,
xlab="Time: (secs since 1970)",
ylab="Counts/min",
type="l",
ylim=(ymin,ymax)
)
robj.dev_off()
import imghdr
imgtype = imghdr.what(tmpgraphfile)
logobject.debug("DataHandler.generateCountsGraph(): OK: What is our tempfile? = %s" % tmpgraphfile )
f = open(tmpgraphfile)
else:
logobject.debug("DataHandler.generateCountsGraph(): No data. Generating proper error image...")
#logobject.debug("DataHandler.generateCountsGraph(): Temp error image filename = %s" % tmpgraphfile)
#import Image
#import imghdr
#imf = Image.open(self.config.get('data','nodatapng'))
#imf.save(tmpgraphfile)
#imgtype = imghdr.what(tmpgraphfile)
#logobject.debug("DataHandler.generateCountsGraph(): ERROR: What is our tempfile? = %s" % imgtype )
f = open(self.config.get('data','nodatapng'))
return f
for cond in data_raw[1][20:]:
if cond == 'brigh':
Cond.append(0)
elif cond == 'undef':
Cond.append(1)
elif cond == 'dark':
Cond.append(2)
C = 3
RT = map(float, data_raw[4][20:])
for i in range(0,len(RT)):
if data_raw[2][20:][i] == 'a':
RT[i] = - float(RT[i])
N = len(RT)
# Create model and sample from it
M = pymc.MCMC(wiener_model(RT, Cond, N, C))
M.sample(iter=5000, burn=0, thin=1)
# plot results with R
from rpy import r
r.x11()
r('par(mfrow=c(3,1))')
r.plot(M.trace('delta_0')[:], col="deepskyblue3", type="l", xlab="", ylab="")
r.plot(M.trace('delta_1')[:], col="deepskyblue3", type="l", xlab="", ylab="")
r.plot(M.trace('delta_2')[:], col="deepskyblue3", type="l", xlab="", ylab="")
r.x11()
r('par(mfrow=c(3,1))')
r.plot(r.density(M.trace('delta_0')[:]), col="deepskyblue4", type="l", xlab="", ylab="", xlim=[-3,3])
r.plot(r.density(M.trace('delta_1')[:]), col="deepskyblue4", type="l", xlab="", ylab="", xlim=[-3,3])
r.plot(r.density(M.trace('delta_2')[:]), col="deepskyblue4", type="l", xlab="", ylab="", xlim=[-3,3])
for S in (S, ):
StructCorr.calcSk(S)
v_kmag = StructCorr.kmags()
v_sk = StructCorr.SkAverages()
#thisRun.sort()
print "top modes:"
print "%6s %6s %7s %9s"%('kmag', 'Sk', 'kmag/L', 'L/kmag')
for Sk, kmag in zip(v_sk, v_kmag)[-10:]:
print "%6.3f %6.3f %7.5f %9.5f"%(kmag, Sk, kmag/L, L/kmag)
r.plot(v_kmag, v_sk,
xlab="", ylab="", type="l",
ylim=(0., 15)
#ylim=(0., 15000)
)
# plots a line at each k-vector point.
for kmag in v_kmag:
r.abline(v=kmag, lty=3, col="lightgray")
# plots each individual k-vector
for kmag, SkArray in zip(v_kmag, StructCorr.SkArrays()):
r.points(x=[kmag]*len(SkArray), y=SkArray,
col="blue", pch="x")
# plots the standard deviation of the by-kvector lists.
for kmag, SkArray in zip(v_kmag, StructCorr.SkArrays()):
r.points(x=kmag, y=numpy.std(SkArray),
col="red", pch="s")
# plots it using the average of all k-vectors -- this should line up
# exactly
def plot(outfile, data, out_format='png'):
w = int(round(len(data) / 4.0))
if out_format == 'png':
r.png(outfile, width=w * 100, height=1000, res=72)
elif out_format == 'pdf':
r.pdf(outfile, width=w, height=10)
else:
raise Exception('Unrecognised format: ' + str(out_format))
print("total: " + str(len(data)))
series = []
points = {'translate': [], 'preprocessing': []}
for dat in data:
points['translate'].append(float(dat['translate']))
points['preprocessing'].append(float(dat['preprocessing']))
xlabels = []
for k, v in data[0].iteritems():
if k not in ["problem", 'translate', 'preprocessing']:
series.append(k)
points[k] = []
index = 0
for dat in data:
for k in series:
if dat[k] != 'no-plan':
points[k].append(float(dat[k]) + \
points['translate'][index] + \
points['preprocessing'][index])
else:
points[k].append(-1000)
xlabels.append(dat['problem'])
index += 1
max_value = max(iter([max(iter(points[k])) for k in series]))
yrange = (0, max_value)
legend_labels = []
x = [i for i in range(1, len(points['translate']) + 1)]
y = [-1000 for i in x]
r.par(mar=(7, 5, 4, 2))
r.plot(x,
y,
main='',
xlab="",
ylab='',
xaxt='n',
yaxt='n',
pch=0,
ylim=yrange,
mgp=(5, 1, 0))
r.mtext("Problem", side=1, line=5)
r.mtext("CPU Time (s)", side=2, line=3)
pch_start = 1
pch_index = pch_start
# plotting "translate"
#r.plot(x, points['translate'], main='',
# xlab='', ylab='Time (s)',
# xaxt='n', yaxt='n',
# pch=0, ylim=yrange)
#legend_labels.append('translate')
r.lines(x, points['translate'], lty=1)
# preprocessing -- Removed since it's insignificant
#r.points(x, points['preprocessing'], pch=pch_index)
#pch_index =+ 1
# planner output
for k in series:
if k != 'translate' and k != 'preporcessing':
r.points(x, points[k], pch=pch_index)
pch_index += 1
legend_labels.append("FD+" + k.upper())
# put x-axis labels
for i in range(0, len(xlabels)):
r.axis(side=1, at=i + 1, labels=xlabels[i], las=2)
# put y-axis labels
base, step = get_y_step(max_value)
print("base: " + str(base) + " -- step: " + str(step))
y = base
for i in range(0, step):
r.axis(side=2, at=y, labels=str(y), las=2)
y += base
# legend
r.legend(1,
max_value,
legend_labels,
pch=[i for i in range(pch_start, pch_index)])
r.dev_off()
from rpy import r
my_x = [5.05, 6.75, 3.21, 2.66]
my_y = [1.65, 26.5, -5.93, 7.96]
ls_fit = r.lsfit(my_x,my_y)
gradient = ls_fit['coefficients']['X']
yintercept= ls_fit['coefficients']['Intercept']
r.png("scatter_regression.png", width=400, height=350)
r.plot(x=my_x, y=my_y, xlab="x", ylab="y", xlim=(0,7), ylim=(-16,27),
main="Example Scatter with regression")
r.abline(a=yintercept, b=gradient, col="red")
r.dev_off()
# Store all the plotting data
data = []
# Print which is used
print "Using:", cp.fullname
# Plot the required output
r.pdf(options.output, width=options.width, height=options.height)
r.par(cex=options.cex)
inv_beta = arange(options.inv_beta_min, options.inv_beta_max, 0.01)
beta = 1.0/inv_beta
lnZ = vectorize(cp.lnZ)(beta)
r.plot(inv_beta, lnZ, type='l', xlab=r("expression(beta**-1)"), ylab=r("""expression(paste("ln ", Z(beta)))"""))
data.append((cp.number, "lnZ", (inv_beta, lnZ)))
betaF = vectorize(cp.betaF)(beta)
r.plot(inv_beta, betaF, type='l', xlab=r("expression(beta**-1)"), ylab=r("expression(F(beta) * beta)"))
data.append((cp.number, "betaF", (inv_beta, betaF)))
S = vectorize(cp.S)(beta)
r.plot(inv_beta, S, type='l', xlab=r("expression(beta**-1)"), ylab=r("expression(S(beta) / k[B])"))
data.append((cp.number, "S", (inv_beta, S)))
E = vectorize(cp.E)(beta)
r.plot(inv_beta, E, type='l', xlab=r("expression(beta**-1)"), ylab=r("expression(bar(E)(beta))"))
data.append((cp.number, "E", (inv_beta, E)))
C = vectorize(cp.C)(beta)
education and they could have different salaries.
'''
education_years = [19,20,16,16,18,12,14,12,16,17];
income = [125000,100000,40000, 35000, 41000, 29000, 35000, 24000, 50000, 60000];
# do the scatter plot
# Specify the output picture size and format.
print "Writing output graph to file: scatterplot.png"
print "To view it in Linux, you can use the File Browser and double-click."
print "For command-line viewing, use the gthumb image viewer as follows:"
print "% gthumb scatterplot.png"
r.png("scatterplot.png", width=400, height=350);
# Draw the plot. xlim and ylim specify the range for the axis. We
# prefer to keep the graph origin at 0,0.
r.plot(x=education_years, y=income, xlab="Education Years", ylab = "Income",
main = "Scatter Plot with Least Squares Fit");
# Compute the least-square fit object between education_years and income.
leastsquarefit = r.lsfit(education_years, income);
#print "leastsquarefit = ", leastsquarefit; # for debugging.
# Compute the slope of the line and the y-intercept from the least-square
# fit object.
gradient = leastsquarefit['coefficients']['X'];
yintercept = leastsquarefit['coefficients']['Intercept'];
# Now plot the least square fit line.
r.abline(a=yintercept, b=gradient, col="red");
# Now turn off the graphics device. This is a R operation to "close"
# the graph.
def plotBundle(self, bundleD, full_filename, colorsD=None, bundlePointsD=None, legendL=None, title=None, y_max=None):
if y_max is None:
y_max = 0.4
if legendL is None:
legendL = bundleD.keys()
legendL.sort()
if title is None:
title = 'data'
bundleIdL = bundleD.keys()
bundleIdL.sort()
if colorsD is None:
colorsL = r.rainbow(len(bundleIdL))
colorsD = dict(zip(bundleIdL, colorsL))
colorsL = [colorsD[x] for x in bundleIdL]
time_min = min([len(bundleD[x]) for x in bundleD.keys()])
timeVec = [0.5 * x for x in range(time_min)]
try:
r.png(full_filename, width=800, height=600)
oldPar = r.par(xpd = True, mar = [x + y for (x,y) in zip(r.par()['mar'], [0,0,0,6])])
print 'plot %s' % full_filename
r.plot(timeVec, timeVec,
type='n',
main=title, ylim=(0, y_max),
xlab="time in hours after transfection", ylab="Relative Cell Counts",
pch=20, lwd=1, lty = 1,
cex=1.0, cex_lab=1.2, cex_main=1.5)
for bundleId in bundleIdL:
if not bundlePointsD is None:
r.points(timeVec, bundlePointsD[bundleId],
col=colorsD[bundleId], pch=20,
lwd=1)
r.lines(timeVec, bundlePointsD[bundleId],
col=colorsD[bundleId],
lwd=1, lty = 1)
r.lines(timeVec, bundleD[bundleId],
col=colorsD[bundleId],
lwd=3, lty = 1)
r.legend(max(timeVec) * 1.1, y_max, legend=legendL, fill=colorsL, cex=1.0, bg= 'whitesmoke')
r.par(oldPar)
r.grid(col="darkgrey")
r.dev_off()
except:
r.dev_off()
print full_filename + ' has not been printed.'
return
def plot(outfile, data, out_format='png'):
w = int(round(len(data)/4.0))
if out_format == 'png':
r.png(outfile, width=w*100, height=1000, res=72)
elif out_format == 'pdf':
r.pdf(outfile, width=w, height=10)
else:
raise Exception('Unrecognised format: ' + str(out_format))
print("total: " + str(len(data)))
series = []
points = {'translate': [], 'preprocessing': []}
for dat in data:
points['translate'].append(float(dat['translate']))
points['preprocessing'].append(float(dat['preprocessing']))
xlabels = []
for k, v in data[0].iteritems():
if k not in ["problem", 'translate', 'preprocessing']:
series.append(k)
points[k] = []
index = 0
for dat in data:
for k in series:
if dat[k] != 'no-plan':
points[k].append(float(dat[k]) + \
points['translate'][index] + \
points['preprocessing'][index])
else:
points[k].append(-1000)
xlabels.append(dat['problem'])
index += 1
max_value = max(iter([max(iter(points[k])) for k in series]))
yrange = (0, max_value)
legend_labels = []
x = [i for i in range(1,len(points['translate'])+1)]
y = [-1000 for i in x]
r.par(mar=(7,5,4,2))
r.plot(x, y, main='', xlab="", ylab='',
xaxt='n', yaxt='n', pch=0, ylim=yrange,
mgp=(5,1,0))
r.mtext("Problem", side=1, line=5)
r.mtext("CPU Time (s)", side=2, line=3)
pch_start = 1
pch_index = pch_start
# plotting "translate"
#r.plot(x, points['translate'], main='',
# xlab='', ylab='Time (s)',
# xaxt='n', yaxt='n',
# pch=0, ylim=yrange)
#legend_labels.append('translate')
r.lines(x, points['translate'], lty=1)
# preprocessing -- Removed since it's insignificant
#r.points(x, points['preprocessing'], pch=pch_index)
#pch_index =+ 1
# planner output
for k in series:
if k != 'translate' and k != 'preporcessing':
r.points(x, points[k], pch=pch_index)
pch_index += 1
legend_labels.append("FD+" + k.upper())
# put x-axis labels
for i in range(0, len(xlabels)):
r.axis(side=1, at=i+1, labels=xlabels[i], las=2)
# put y-axis labels
base, step = get_y_step(max_value)
print("base: " + str(base) + " -- step: " + str(step))
y = base
for i in range(0, step):
r.axis(side=2, at=y, labels=str(y), las=2)
y += base
# legend
r.legend(1, max_value, legend_labels, pch=[i for i in range(pch_start, pch_index)])
r.dev_off()
from rpy import r
# first plot
x = range(1,11)
y = [i**2 for i in x]
r.plot(x, y, xlab='x', ylab='y', main='My first plot',
pch=21, col='blue', bg='lightblue', type='o')
# second plot
x = range(1,11)
y = [i**2 for i in x]
z = [i**3 for i in x]
r.plot(x, y, main='My second plot', xlab='x', ylab='y', type='l', col='blue')
r.lines(x, z, col='red')
# cosine function, save to file
import math
r.png('cosine.png')
x = r.seq(0,50, by=0.1)
y = [math.cos(i) for i in x]
r.plot(x, y, main='COS(X)', xlab='x', ylab='cos(x)', type='l', col='blue')
r.dev_off()
# histogram
x = range(10) + range(3,6) + range(5,10)
r.hist(x, main='A histogram', xlab='x', col='lightblue')
# adust plotting area
from rpy import r
from rpy import r
import os.path
# find out where the temp directory is
tempdir = r.tempdir()
# write its name into a file
f = open('tempdir','w')
f.write(tempdir)
f.close()
# put something there..
r.postscript(os.path.join(tempdir,"foo.ps"))
r.plot(1,1)
r.dev_off()
