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 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 create_p_value_boxplot_eps(best_p_values, filename):
from rpy import r
r.postscript(filename, horizontal=False, height=4.5, width=6, pointsize=10)
try:
keys = best_p_values.keys()
keys.sort()
r.boxplot(
map(best_p_values.get, keys),
names=map(str, keys),
xlab="sample size", ylab="p-score")
finally:
r.dev_off()
def create_p_value_boxplot_eps(best_p_values, filename):
from rpy import r
r.postscript(filename, horizontal=False, height=4.5, width=6, pointsize=10)
try:
keys = best_p_values.keys()
keys.sort()
r.boxplot(map(best_p_values.get, keys),
names=map(str, keys),
xlab="sample size",
ylab="p-score")
finally:
r.dev_off()
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
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()
