Re: [Matplotlib-users] patchcollection wihtout edgecolor an d gradient filled patches
>p = PatchCollection(patches, alpha = 1.0,cmap = mpl.cm.Blues, >linewidth="0.0",edgecolor="black",linewidth="0.0") The documentation at http://matplotlib.sourceforge.net /api/collections_api.html#matplotlib.collections.PatchCollection has _plurals_ on the kwards (linewidths rather than linewidth) and as such it works for me: coll=matplotlib.collections.PatchCollection( patches,alpha=.5,linewidths=0.) using matplotlib 0.99.0. HTH, Vaclav -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] graphs in memory
i got that problem solved but i now have a new memory problem, the
error i get is
invalid command name " *randomnumber*callit"
while executing
" *randomnumber*callit"
("after" script)
searched the internet and found that there is some variable stuck
somewhere, here is the def cousing the error, is designed to read some
files (getting them from the lists self.files and self.workspaces)
make a plot and save the plot
def save2dmulti(self):
try:
os.mkdir(self.save+"/graph")
except:
pass
for x in range(0,1):
#fig = pyplot.figure()
for file in self.files:
ax = pyplot.subplot(111)#fig.add_subplot(111)
pyplot.hold(True)
for workspace in self.workspaces:
f = open(workspace+"/alignment.iuf","r")
idlist = pickle.load(f)
f.close()
self.__newdict = {}
for item in idlist:
self.__newdict[idlist[item]] = item
for x in range(0,1):
try:
f =
open(workspace+"/letters/letter_"+self.__newdict[file]+".txt", "r")
except:
print "gene "+file+" not found in
"+workspace+" skipping this workspace"
break
vals = pickle.load(f)
f.close()
base = []
basecount = []
for val in vals:
if val[0] == "A":
base.append("A")
basecount.append(val[1])
elif val[0] == "C":
base.append("C")
basecount.append(val[2])
elif val[0] == "T":
base.append("T")
basecount.append(val[3])
elif val[0] == "G":
base.append("G")
basecount.append(val[4])
N = len(base)
ind = numpy.arange(N)
width = 0.5
ax.plot(ind, basecount,'o-', label = workspace)
ax.set_xticks(ind)
ax.set_title(file)
pyplot.legend()
#print "one"
for workspacer in self.workspaces:
#print "pretry"
try:
#print "opening file"
f = open(workspacer+"/alignment.iuf","r")
idlist = pickle.load(f)
f.close()
#print "making dict"
self.__newdict = {}
for item in idlist:
self.__newdict[idlist[item]] = item
f =
open(workspacer+"/validated/"+self.__newdict[file]+".fa","r")
text = f.read()
text = text.split("\n")
#print text, text[0], text[1]
f.close()
f = open(self.save+"/temp.fa","w")
#print "check OK"+workspacer
t = text[0]+"\n"+text[1]+"\n"
f.write(t)
f.close()
output = ""
cline = "centroid_fold "+self.save+"/temp.fa"
test = subprocess.Popen(str(cline),stdout =
subprocess.PIPE,stderr = open(os.devnull))
output = test.communicate()[0]
#print output
output = output.split(">")
out = output[1]
out = out.split("\r\n")
#print out
xax = []
counter =0
for x in range(0,len(base)):
xax.append(str(vals[counter][0])+"\n"+out[2][counter])
counter = counter +1
ax.set_xticks(ind)
ax.set_xticklabels(xax)
sav = file
sav =
sav.replace(":","_").replace("\\","_").replace("-","_").replace(">","")
#pyplot.show()
pyplot.savefig(self.save+"/graph/"+sav+".png")
os.remove(self.save+"/temp.fa")
pyplot.clf()
break
except:
#print workspacer +" failed"
#print "ERROR"
pass
the code itself works and does what it needs to do, side effect is
that when i later make and show a graph all the graphs made by this
[Matplotlib-users] Problem when specifying formatter
Hi, I'm not sure what I'm doing wrong here: import matplotlib.pyplot as mpl from matplotlib.ticker import NullFormatter fig = mpl.figure() ax = fig.add_subplot(111) ax.xaxis.set_major_formatter(NullFormatter) This returns the error: Traceback (most recent call last): File "test.py", line 6, in ax.xaxis.set_major_formatter(NullFormatter) File "/Users/tom/Library/Python/2.6/site-packages/matplotlib/ axis.py", line 1091, in set_major_formatter formatter.set_axis(self) TypeError: unbound method set_axis() must be called with NullFormatter instance as first argument (got XAxis instance instead) Am I using set_major_formatter wrongly? Thanks, Thomas -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] drawing points on simplex?
http://www.nabble.com/Re%3A-Three-Phase-Diagrams-with-matplotlib-p25122618.html Maybe this is close to what you want? -JJ On Sun, Oct 18, 2009 at 8:23 PM, per freem wrote: > hi all, > > i would like to draw points on the 3-d simplex, like that of a > dirichlet distribution with 3 parameters. in other words, all i want > to draw are three axes that go from 0 to 1 and make a triangular > shape, such that each point on the triangular region the three axes > form uniquely determines a point on the simplex. > > is there an easy way to do this in matplotlib? just to be clear, i > dont want to draw a density/distribution over the simplex, but just > individual points on it. so really all i want are three ordinary axes > that happen to intersect and make a triangle. > > thanks very much. > > -- > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > ___ > Matplotlib-users mailing list > Matplotlib-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-users > -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problem when specifying formatter
On Tue, Oct 20, 2009 at 3:43 PM, Thomas Robitaille wrote: > Hi, > > I'm not sure what I'm doing wrong here: > > import matplotlib.pyplot as mpl > from matplotlib.ticker import NullFormatter > > fig = mpl.figure() > ax = fig.add_subplot(111) > ax.xaxis.set_major_formatter(NullFormatter) > > This returns the error: > > Traceback (most recent call last): > File "test.py", line 6, in > ax.xaxis.set_major_formatter(NullFormatter) > File "/Users/tom/Library/Python/2.6/site-packages/matplotlib/ > axis.py", line 1091, in set_major_formatter > formatter.set_axis(self) > TypeError: unbound method set_axis() must be called with NullFormatter > instance as first argument (got XAxis instance instead) > > Am I using set_major_formatter wrongly? You need to use an *instance* of NullFormatter, which is the name of a class. Try: ax.xaxis.set_major_formatter(NullFormatter()) Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problem when specifying formatter
On Tue, Oct 20, 2009 at 4:43 PM, Thomas Robitaille wrote: > ax.xaxis.set_major_formatter(NullFormatter) http://matplotlib.sourceforge.net/api/axis_api.html?highlight=set_major_formatter#matplotlib.axis.Axis.set_major_formatter An instance of NullFormatter is needed, instead of the class itself. ax.xaxis.set_major_formatter(NullFormatter()) -JJ -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
