Having trouble with aligning subplots

Hello y'all:

I am trying to plot a fig with three subplots. However when I run my
script the subplots are all shifted way too high
(http://img.skitch.com/20090720-fp462u8ww4bq38j29u9bjtr2cx.png) and
the top subplot is cut off.

I tried doing something like this from reading another poster's thread
but this did absolutely nothing:
mpl.figure.SubplotParams(left= (48 / 72.0) / figW, # 48-point left margin
bottom= (36 / 72.0) / figH, # etc.
right= 1 - (18 / 72.0) / figW,
top= 1 - (12 / 72.0) / figH)

Anyone have an idea how to fix this.

Thank you for your time.

Gus

The code is below for those interested:
<code>
supTitle = 'Ortholog Pairs Matching "Real" or "Control" Ag miRNA seeds.'

data = []
for dFile in iFiles:
    data.append(pickle.load(open(dFile,'rU')))

ks = []
for i in range(len(data)):
    ks.append(sorted(data[i].keys()))

for i in range(len(ks)):
    if "!doc" in ks[i]: ks[i].pop(0) # if the pkl has a !doc entry. pop it
    assert odd_or_even(len(ks[i])) == 'even', 'Error: len(ks[i]) must be even.'
pos1Data = eval('[%s]' % ('[],'*len(data)))
pos1Keys = eval('[%s]' % ('[],'*len(data)))
pos2Data = eval('[%s]' % ('[],'*len(data)))
pos2Keys = eval('[%s]' % ('[],'*len(data)))

for i in range(len(ks)):
    for j in range(len(ks[i])):
        if odd_or_even(j) == 'even': # remember that we start with 0
which is even.
            pos1Data[i].append(data[i][ks[i][j]])
            pos1Keys[i].append(ks[i][j])
        else:
            pos2Data[i].append(data[i][ks[i][j]])
            pos2Keys[i].append(ks[i][j])

figW = 16
figH = 8
plt.figure(num=None, figsize=None, dpi=None, facecolor='w', edgecolor='k')
subplotpars=mpl.figure.SubplotParams(left= (48 / 72.0) / figW,
# 48-point left margin
                                     bottom= (36 / 72.0) / figH, # etc.
                                     right= 1 - (18 / 72.0) / figW,
                                     top= 1 - (12 / 72.0) / figH)

plt.suptitle(supTitle)
for i in range(len(data)):
    matches1 = [x[0] for x in pos1Data[i]]
    ctrls1 = [-x[1] for x in pos1Data[i]]
    matches2 = [x[0] for x in pos2Data[i]]
    ctrls2 = [-x[1] for x in pos2Data[i]]

    assert len(matches1) == len(matches2), 'Error: matches1 and
matches 2 do not have the same number of elements!'
    N = len(matches1)

    ind = np.arange(N) # the x locations for the groups
    width = 0.35 # the width of the bars: can also be len(x) sequence

    plt.subplot(len(data),1,i,)
    p1 = plt.bar(ind, ctrls1, width, color='w',)
    p2 = plt.bar(ind, matches1, width, color='b',)
    p3 = plt.bar(ind+width, ctrls2, width, color='w',)
    p4 = plt.bar(ind+width, matches2, width, color='b', )
    plt.ylabel(subTitles[i])
    if i == len(data)-1:
        plt.xlabel('miRNA seed')

    axMax = max(matches1+matches2)*1.1
    axMin = min(ctrls1+ctrls2)*1.1
    #plt.axis([0,len(matches1),axMin,axMax])
    if i == 0:
        plt.legend( (p2[0], p1[0]), ('Real', 'Ctrls'), loc=(1.01,0.65) )
</code>

index for subplot starts from 1, not 0 (the convention is from Matlab).

Regards,

-JJ

···

On Mon, Jul 20, 2009 at 6:31 PM, W. Augustine Dunn III<wadunn83@...287...> wrote:

Hello y'all:

I am trying to plot a fig with three subplots. However when I run my
script the subplots are all shifted way too high
(http://img.skitch.com/20090720-fp462u8ww4bq38j29u9bjtr2cx.png) and
the top subplot is cut off.

I tried doing something like this from reading another poster's thread
but this did absolutely nothing:
mpl.figure.SubplotParams(left= (48 / 72.0) / figW, # 48-point left margin
bottom= (36 / 72.0) / figH, # etc.
right= 1 - (18 / 72.0) / figW,
top= 1 - (12 / 72.0) / figH)

Anyone have an idea how to fix this.

Thank you for your time.

Gus

The code is below for those interested:
<code>
supTitle = 'Ortholog Pairs Matching "Real" or "Control" Ag miRNA seeds.'

data = []
for dFile in iFiles:
data.append(pickle.load(open(dFile,'rU')))

ks = []
for i in range(len(data)):
ks.append(sorted(data[i].keys()))

for i in range(len(ks)):
if "!doc" in ks[i]: ks[i].pop(0) # if the pkl has a !doc entry. pop it
assert odd_or_even(len(ks[i])) == 'even', 'Error: len(ks[i]) must be even.'
pos1Data = eval('[%s]' % ('[],'*len(data)))
pos1Keys = eval('[%s]' % ('[],'*len(data)))
pos2Data = eval('[%s]' % ('[],'*len(data)))
pos2Keys = eval('[%s]' % ('[],'*len(data)))

for i in range(len(ks)):
for j in range(len(ks[i])):
if odd_or_even(j) == 'even': # remember that we start with 0
which is even.
pos1Data[i].append(data[i][ks[i][j]])
pos1Keys[i].append(ks[i][j])
else:
pos2Data[i].append(data[i][ks[i][j]])
pos2Keys[i].append(ks[i][j])

figW = 16
figH = 8
plt.figure(num=None, figsize=None, dpi=None, facecolor='w', edgecolor='k')
subplotpars=mpl.figure.SubplotParams(left= (48 / 72.0) / figW,
# 48-point left margin
bottom= (36 / 72.0) / figH, # etc.
right= 1 - (18 / 72.0) / figW,
top= 1 - (12 / 72.0) / figH)

plt.suptitle(supTitle)
for i in range(len(data)):
matches1 = [x[0] for x in pos1Data[i]]
ctrls1 = [-x[1] for x in pos1Data[i]]
matches2 = [x[0] for x in pos2Data[i]]
ctrls2 = [-x[1] for x in pos2Data[i]]

assert len(matches1) == len(matches2), 'Error: matches1 and
matches 2 do not have the same number of elements!'
N = len(matches1)

ind = np.arange(N) # the x locations for the groups
width = 0.35 # the width of the bars: can also be len(x) sequence

plt.subplot(len(data),1,i,)
p1 = plt.bar(ind, ctrls1, width, color='w',)
p2 = plt.bar(ind, matches1, width, color='b',)
p3 = plt.bar(ind+width, ctrls2, width, color='w',)
p4 = plt.bar(ind+width, matches2, width, color='b', )
plt.ylabel(subTitles[i])
if i == len(data)-1:
plt.xlabel('miRNA seed')

axMax = max(matches1+matches2)*1.1
axMin = min(ctrls1+ctrls2)*1.1
#plt.axis([0,len(matches1),axMin,axMax])
if i == 0:
plt.legend( (p2[0], p1[0]), ('Real', 'Ctrls'), loc=(1.01,0.65) )
</code>

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Thanks!

···

On Mon, Jul 20, 2009 at 3:44 PM, Jae-Joon Lee<lee.j.joon@...287...> wrote:

index for subplot starts from 1, not 0 (the convention is from Matlab).

Regards,

-JJ

On Mon, Jul 20, 2009 at 6:31 PM, W. Augustine Dunn > III<wadunn83@...287...> wrote:

Hello y'all:

I am trying to plot a fig with three subplots. However when I run my
script the subplots are all shifted way too high
(http://img.skitch.com/20090720-fp462u8ww4bq38j29u9bjtr2cx.png) and
the top subplot is cut off.

I tried doing something like this from reading another poster's thread
but this did absolutely nothing:
mpl.figure.SubplotParams(left= (48 / 72.0) / figW, # 48-point left margin
bottom= (36 / 72.0) / figH, # etc.
right= 1 - (18 / 72.0) / figW,
top= 1 - (12 / 72.0) / figH)

Anyone have an idea how to fix this.

Thank you for your time.

Gus

The code is below for those interested:
<code>
supTitle = 'Ortholog Pairs Matching "Real" or "Control" Ag miRNA seeds.'

data = []
for dFile in iFiles:
data.append(pickle.load(open(dFile,'rU')))

ks = []
for i in range(len(data)):
ks.append(sorted(data[i].keys()))

for i in range(len(ks)):
if "!doc" in ks[i]: ks[i].pop(0) # if the pkl has a !doc entry. pop it
assert odd_or_even(len(ks[i])) == 'even', 'Error: len(ks[i]) must be even.'
pos1Data = eval('[%s]' % ('[],'*len(data)))
pos1Keys = eval('[%s]' % ('[],'*len(data)))
pos2Data = eval('[%s]' % ('[],'*len(data)))
pos2Keys = eval('[%s]' % ('[],'*len(data)))

for i in range(len(ks)):
for j in range(len(ks[i])):
if odd_or_even(j) == 'even': # remember that we start with 0
which is even.
pos1Data[i].append(data[i][ks[i][j]])
pos1Keys[i].append(ks[i][j])
else:
pos2Data[i].append(data[i][ks[i][j]])
pos2Keys[i].append(ks[i][j])

figW = 16
figH = 8
plt.figure(num=None, figsize=None, dpi=None, facecolor='w', edgecolor='k')
subplotpars=mpl.figure.SubplotParams(left= (48 / 72.0) / figW,
# 48-point left margin
bottom= (36 / 72.0) / figH, # etc.
right= 1 - (18 / 72.0) / figW,
top= 1 - (12 / 72.0) / figH)

plt.suptitle(supTitle)
for i in range(len(data)):
matches1 = [x[0] for x in pos1Data[i]]
ctrls1 = [-x[1] for x in pos1Data[i]]
matches2 = [x[0] for x in pos2Data[i]]
ctrls2 = [-x[1] for x in pos2Data[i]]

assert len(matches1) == len(matches2), 'Error: matches1 and
matches 2 do not have the same number of elements!'
N = len(matches1)

ind = np.arange(N) # the x locations for the groups
width = 0.35 # the width of the bars: can also be len(x) sequence

plt.subplot(len(data),1,i,)
p1 = plt.bar(ind, ctrls1, width, color='w',)
p2 = plt.bar(ind, matches1, width, color='b',)
p3 = plt.bar(ind+width, ctrls2, width, color='w',)
p4 = plt.bar(ind+width, matches2, width, color='b', )
plt.ylabel(subTitles[i])
if i == len(data)-1:
plt.xlabel('miRNA seed')

axMax = max(matches1+matches2)*1.1
axMin = min(ctrls1+ctrls2)*1.1
#plt.axis([0,len(matches1),axMin,axMax])
if i == 0:
plt.legend( (p2[0], p1[0]), ('Real', 'Ctrls'), loc=(1.01,0.65) )
</code>

------------------------------------------------------------------------------
Enter the BlackBerry Developer Challenge
This is your chance to win up to $100,000 in prizes! For a limited time,
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize
details at: http://p.sf.net/sfu/Challenge
_______________________________________________
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users

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