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 plot(self, vector_list, gene_id_list):
self.no_of_curves = 0
x_range = (1, len(vector_list[0]))
y_range = self.get_min_max(vector_list)
r.postscript("%s"%self.plot_file)
for vector in vector_list:
(x_list, y_list) = self.xy_list_return(vector)
self._plot(x_list, y_list, x_range, y_range)
r.legend(x_range[1], y_range[1], gene_id_list, col=range(1, self.no_of_curves+1), lty=1, pch='*', xjust=1)
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):
#this function deals with 3 fixed parameters and 1 varying parameter
self.curs.execute("select distinct %s, %s, %s, %s, tag from\
stat_plot_data where %s=%s and %s=%s and %s=%s and tag='%s' order by %s \
"%(self.option_num_dict[0].label, self.option_num_dict[1].label, self.option_num_dict[2].label,\
self.option_num_dict[3].label, 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.tag, self.option_num_dict[3].label))
rows = self.curs.fetchall()
r.png('%s'%self.ofname)
for row in rows:
#position 0,1,2 are fixed values, 3 is varying value, 4 is the tag value.
self._plot(row)
#add the legend
r.legend(self.x_range[1], self.y_range[1], self.varying_list, col=range(1, self.no_of_curves+1), lty=1, pch='*', xjust=1)
r.dev_off()
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 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()
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()
