Develop Reference

Matplotlib Draw a Constant y Axis

I want to use matpoltlib to make a plot that with a constant y axis(always from 0 to 14 and the gap is 1), since I want to make labels for them and my dot values will be(x, y) where y is from 0 to 14 gap 1, and a changing x axis. I already tried to play with y ticks. And here is my code for that:
fig, ax = plt.subplots()
fig.canvas.draw()
plt.yticks(np.arange(0, 14, 1))
labels = [item.get_text() for item in ax.get_yticklabels()]
labels[1] = 'Not Detected'
labels[2] = 'A/G'
labels[3] = 'G/G'
labels[4] = 'C/T'
labels[5] = 'C/C'
labels[6] = 'A/A'
labels[7] = '-1'
labels[8] = 'ε3/ε3'
labels[9] = 'A/C'
labels[10] = 'T/T'
labels[11] = 'C/G'
labels[12] = 'ε2/ε3'
labels[13] = 'G/T'
ax.set_yticklabels(labels)
what I'm thinking about is to use some values or lines with white color so those y axis will appear. But I'm looking for a more efficient way of doing it. And here is the diagram I generated with the current code. It only shows C/C right now and I want all labels to appear in the diagram.
I tried draw white points with:
x1 = np.arange(n)
y1 = np.arange(1,15,1)
plt.scatter(x1,y1,color = 'white')
Which did give me what I want: But I was wondering whether there is a lib setting that can do this.

I would recommend just using a fixed locator and fixed formatter for your y axis. The function, ax.set_yticklabels() is simply a convenience wrapper for these tick methods.
I would also recommend having your y_labels in a list or using a loop structure as this is a more generalizable and modifiable implementation.
If I'm understanding the goals of your plot correctly, something like this may work well for you.
import matplotlib.pyplot as plt
import numpy as np
import matplotlib as mpl
#make some data
x = np.arange(25)
y = np.random.randint(1, 14, size=25)
#convert y labels to a list
y_labels = [
'Not Detected','A/G','G/G','C/T','C/C','A/A',
'-1','ε3/ε3', 'A/C','T/T','C/G','ε2/ε3','G/T'
]
#define figure/ax and set figsize
fig, ax = plt.subplots(figsize=(12,8))
#plot data, s is marker size, it's points squared
ax.scatter(x, y, marker='x', s=10**2, color='#5d2287', linewidth=2)
#set major locator and formatter to fixed, add grid, hide top/right spines
locator = ax.yaxis.set_major_locator(mpl.ticker.FixedLocator(np.arange(1, 14)))
formatter = ax.yaxis.set_major_formatter(mpl.ticker.FixedFormatter(y_labels))
grid = ax.grid(axis='y', dashes=(8,3), alpha=0.3, color='gray')
spines = [ax.spines[x].set_visible(False) for x in ['top','right']]
params = ax.tick_params(labelsize=12) #increase label font size

Make legend stay at bottom matplotlib python

I have a graph with about 30 different curves and I want to show them all in the legend. But it gets too long and they don't all fit. I want to put them down the bottom, how do I do this?
fig = plt.figure()
for i in range(len(data)):
print(i)
x1 = data.loc[0][5:-4]
y1 = data.loc[i][5:-4]
y1.replace(' ',100.0,inplace=True)
x = list(reversed(x1))
y = list(reversed(y1))
report_num = data.loc[i,'Report No']
plt.plot(x, y, label = report_num)
plt.xscale('log')
plt.grid()
plt.yticks(yints)
plt.xticks(x,x,rotation=40)
plt.title('Particle Size Distribution Curve - %s'%(report_num))
plt.legend(loc=1)

np.polyfit does not fit the data

I can not find a curve that adjust the data (lists 'chi' and 'm'). I used polyfit to generate the curve but it was not enough to capture the behavior of the points.
The code ahead has a plot that shows the discrepancy between the data and the adjustment.
import matplotlib.pyplot as plt
import numpy as np
chi = [159.227326193538,157.045536099339,154.874421083320,152.714227953804,150.565205206850,148.427603026261,146.301673283577,144.187669538078,142.085847036787,139.996462714462,137.919775193605,135.856044784456,133.805533484994,131.768504980940,129.745224645753,127.735959540633,125.740978414520,123.760551704092,121.794951533770,119.844451715712,117.909327749816,115.989856823722,114.086317812809,112.198991280194,110.328159476736,108.474106341033,106.637117499424,104.817480265986,103.015483642536,101.231418318633,99.4655766715733,97.7182527663948,95.9897423558747,94.2803428805298,92.5903534686167,90.9200749361326,89.2698097868135,87.6398622121363,86.0305380913169,84.4421449913117,82.8749921668166,81.3293905602669,79.8056528018393,78.3040932094484,76.8250277887500,75.3687742331392,73.9356519237512,72.5259819294609,71.1400870068830,69.7782916003724,68.4409218420233,67.1283055516702,65.8407722368873,64.5786530929887,63.3422810030283,62.1319905377998,60.9481179558368,59.7910012034130,58.6609799145416,57.5583954109757,56.4835907022086,55.4369104854728,54.4187011457414,53.4293107557267,52.4690890758814,51.5383875543978,50.6375593272080,49.7669592179839,48.9269437381375,48.1178710868206,47.3401011509247,46.5939955050811,45.8799174116612,45.1982318207762,44.5493053702771,43.9335063857545,43.3512048805394,42.8027725557022,42.2885828000534,41.8090106901432,41.3644329902617,40.9552281524389,40.5817763164445,40.2444593097885,39.9436606477201,39.6797655332288,39.4531608570438,39.2642351976343,39.1133788212092,39.0009836817171,38.9274434208471,38.8931533680273,38.8985105404262,38.9439136429520,39.0297630682529,39.1564608967166,39.3244108964711,39.5340185233838,39.7856909210623,40.0798369208539,40.4168670418459,40.7971934908652,41.2212301624788,41.6893926389935,42.2020981904556,42.7597657746519,43.3628160371087,44.0116713110920,44.7067556176079,45.4484946654022,46.2373158509606,47.0736482585089,47.9579226600125,48.8905715151762,49.8720289714460,50.9027308640062,51.9831147157818,53.1136197374377,54.2946868273783,55.5267585717480,56.8102792444312,58.1456948070521,59.5334529089743,60.9740028873018,62.4677957668786,64.0152842602876,65.6169227678529,67.2731673776373,68.9844758654438,70.7513076948157,72.5741240170354,74.4533876711260,76.3895631838499,78.3831167697092,80.4345163309464,82.5442314575433,84.7127334272220,86.9404952054444,89.2279914454118,91.5756984880661,93.9840943620883,96.4536587839001,98.9848731576614,101.578220575274,104.234185816379,106.953255348357,109.735917326327,112.582661593151,115.493979679428,118.470364803498,121.512311871442,124.620317477080,127.794879901969,131.036499115411,134.345676774445,137.722916223849,141.168722496142,144.683602311584,148.268064078173,151.922617891649,155.647775535488,159.444050480909,163.311957886871,167.252014600072,171.264739154948,175.350651773679,179.510274366181,183.744130530113,188.052745550870,192.436646401591,196.896361743152,201.432421924170,206.045358981001,210.735706637743,215.504000306232,220.350777086043,225.276575764494,230.281936816639,235.367402405274,240.533516380936,245.780824281900,251.109873334181,256.521212451534,262.015392235454,267.592964975176,273.254484647676,279.000506917667,284.831589137604,290.748290347682,296.751171275834,302.840794337735,309.017723636798,315.282524964177,321.635765798766,328.078015307199,334.609844343848,341.231825450827,347.944532857988,354.748542482925,361.644431930971,368.632780495196]
m=[-1,-0.990000000000000,-0.980000000000000,-0.970000000000000,-0.960000000000000,-0.950000000000000,-0.940000000000000,-0.930000000000000,-0.920000000000000,-0.910000000000000,-0.900000000000000,-0.890000000000000,-0.880000000000000,-0.870000000000000,-0.860000000000000,-0.850000000000000,-0.840000000000000,-0.830000000000000,-0.820000000000000,-0.810000000000000,-0.800000000000000,-0.790000000000000,-0.780000000000000,-0.770000000000000,-0.760000000000000,-0.750000000000000,-0.740000000000000,-0.730000000000000,-0.720000000000000,-0.710000000000000,-0.700000000000000,-0.690000000000000,-0.680000000000000,-0.670000000000000,-0.660000000000000,-0.650000000000000,-0.640000000000000,-0.630000000000000,-0.620000000000000,-0.610000000000000,-0.600000000000000,-0.590000000000000,-0.580000000000000,-0.570000000000000,-0.560000000000000,-0.550000000000000,-0.540000000000000,-0.530000000000000,-0.520000000000000,-0.510000000000000,-0.500000000000000,-0.490000000000000,-0.480000000000000,-0.470000000000000,-0.460000000000000,-0.450000000000000,-0.440000000000000,-0.430000000000000,-0.420000000000000,-0.410000000000000,-0.400000000000000,-0.390000000000000,-0.380000000000000,-0.370000000000000,-0.360000000000000,-0.350000000000000,-0.340000000000000,-0.330000000000000,-0.320000000000000,-0.310000000000000,-0.300000000000000,-0.290000000000000,-0.280000000000000,-0.270000000000000,-0.260000000000000,-0.250000000000000,-0.240000000000000,-0.230000000000000,-0.220000000000000,-0.210000000000000,-0.200000000000000,-0.190000000000000,-0.180000000000000,-0.170000000000000,-0.160000000000000,-0.150000000000000,-0.140000000000000,-0.130000000000000,-0.120000000000000,-0.110000000000000,-0.100000000000000,-0.0900000000000000,-0.0800000000000000,-0.0700000000000000,-0.0599999999999999,-0.0499999999999999,-0.0400000000000000,-0.0300000000000000,-0.0200000000000000,-0.0100000000000000,0,0.0100000000000000,0.0200000000000000,0.0300000000000000,0.0400000000000000,0.0499999999999999,0.0599999999999999,0.0700000000000000,0.0800000000000000,0.0900000000000000,0.100000000000000,0.110000000000000,0.120000000000000,0.130000000000000,0.140000000000000,0.150000000000000,0.160000000000000,0.170000000000000,0.180000000000000,0.190000000000000,0.200000000000000,0.210000000000000,0.220000000000000,0.230000000000000,0.240000000000000,0.250000000000000,0.260000000000000,0.270000000000000,0.280000000000000,0.290000000000000,0.300000000000000,0.310000000000000,0.320000000000000,0.330000000000000,0.340000000000000,0.350000000000000,0.360000000000000,0.370000000000000,0.380000000000000,0.390000000000000,0.400000000000000,0.410000000000000,0.420000000000000,0.430000000000000,0.440000000000000,0.450000000000000,0.460000000000000,0.470000000000000,0.480000000000000,0.490000000000000,0.500000000000000,0.510000000000000,0.520000000000000,0.530000000000000,0.540000000000000,0.550000000000000,0.560000000000000,0.570000000000000,0.580000000000000,0.590000000000000,0.600000000000000,0.610000000000000,0.620000000000000,0.630000000000000,0.640000000000000,0.650000000000000,0.660000000000000,0.670000000000000,0.680000000000000,0.690000000000000,0.700000000000000,0.710000000000000,0.720000000000000,0.730000000000000,0.740000000000000,0.750000000000000,0.760000000000000,0.770000000000000,0.780000000000000,0.790000000000000,0.800000000000000,0.810000000000000,0.820000000000000,0.830000000000000,0.840000000000000,0.850000000000000,0.860000000000000,0.870000000000000,0.880000000000000,0.890000000000000,0.900000000000000,0.910000000000000,0.920000000000000,0.930000000000000,0.940000000000000,0.950000000000000,0.960000000000000,0.970000000000000,0.980000000000000,0.990000000000000,1]
poly = np.polyfit(chi, m, deg = 40)
fit_fn = np.poly1d(poly)
f = plt.figure()
ax = f.add_subplot(111)
ax.plot(m, chi, 'r-', label = 'data')
ax.plot(fit_fn(chi), chi, 'b-', label = 'adjust')
ax.set_xlabel('$m$')
ax.set_ylabel('$\chi^2$')
plt.legend()
plt.show()
plt.close()

The problem is that you mixed the x and the y coordinates while fitting and plotting the fit. Since m is the x-coordinate (independent variable) and chi is the y-coordinate (dependent variable), pass them in the right order. The lines modified are indicated by a comment #
poly = np.polyfit(m, chi, deg = 4) # <-----
fit_fn = np.poly1d(poly)
f = plt.figure()
ax = f.add_subplot(111)
ax.plot(m, chi, 'rx', label = 'data') # <---- Just used x to plot symbols
ax.plot(m, fit_fn(m), 'b-', lw=2, label = 'adjust') # <-----
ax.set_xlabel('$m$')
ax.set_ylabel('$\chi^2$')
plt.legend()
plt.show()
plt.close()

Laying out several plots in matplotlib + numpy

I am pretty new to python and want to plot a dataset using a histogram and a heatmap below. However, I am a bit confused about
How to put a title above both plots and
How to insert some text into bots plots
How to reference the upper and the lower plot
For my first task I used the title instruction, which inserted a caption in between both plots instead of putting it above both plots
For my second task I used the figtext instruction. However, I could not see the text anywhere in the plot. I played a bit with the x, y and fontsize parameters without any success.
Here is my code:
def drawHeatmap(xDim, yDim, plot, threshold, verbose):
global heatmapList
stableCells = 0
print("\n[I] - Plotting Heatmaps ...")
for currentHeatmap in heatmapList:
if -1 in heatmapList[currentHeatmap]:
continue
print("[I] - Plotting heatmap for PUF instance", currentHeatmap,"(",len(heatmapList[currentHeatmap])," values)")
# Convert data to ndarray
#floatMap = list(map(float, currentHeatmap[1]))
myArray = np.array(heatmapList[currentHeatmap]).reshape(xDim,yDim)
# Setup two plots per page
fig, ax = plt.subplots(2)
# Histogram
weights = np.ones_like(heatmapList[currentHeatmap]) / len(heatmapList[currentHeatmap])
hist, bins = np.histogram(heatmapList[currentHeatmap], bins=50, weights=weights)
width = 0.7 * (bins[1] - bins[0])
center = (bins[:-1] + bins[1:]) / 2
ax[0].bar(center, hist, align='center', width=width)
stableCells = calcPercentageStable(threshold, verbose)
plt.figtext(100,100,"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!", fontsize=40)
heatmap = ax[1].pcolor(myArray, cmap=plt.cm.Blues, alpha=0.8, vmin=0, vmax=1)
cbar = fig.colorbar(heatmap, shrink=0.8, aspect=10, fraction=.1,pad=.01)
#cbar.ax.tick_params(labelsize=40)
for y in range(myArray.shape[0]):
for x in range(myArray.shape[1]):
plt.text(x + 0.5, y + 0.5, '%.2f' % myArray[y, x],
horizontalalignment='center',
verticalalignment='center',
fontsize=(xDim/yDim)*5
)
#fig = plt.figure()
fig = matplotlib.pyplot.gcf()
fig.set_size_inches(60.5,55.5)
plt.savefig(dataDirectory+"/"+currentHeatmap+".pdf", dpi=800, papertype="a3", format="pdf")
#plt.title("Heatmap for PUF instance "+str(currentHeatmap[0][0])+" ("+str(numberOfMeasurements)+" measurements; "+str(sizeOfMeasurements)+" bytes)")
if plot:
plt.show()
print("\t[I] - Done ...")
And here is my current output:

Perhaps this example will make things easier to understand. Things to note are:
Use fig.suptitle to add a title to the top of a figure.
Use ax[i].text(x, y, str) to add text to an Axes object
Each Axes object, ax[i] in your case, holds all the information about a single plot. Use them instead of calling plt, which only really works well with one subplot per figure or to modify all subplots at once. For example, instead of calling plt.figtext, call ax[0].text to add text to the top plot.
Try following the example code below, or at least read through it to get a better idea how to use your ax list.
import numpy as np
import matplotlib.pyplot as plt
histogram_data = np.random.rand(1000)
heatmap_data = np.random.rand(10, 100)
# Set up figure and axes
fig = plt.figure()
fig.suptitle("These are my two plots")
top_ax = fig.add_subplot(211) #2 rows, 1 col, 1st plot
bot_ax = fig.add_subplot(212) #2 rows, 1 col, 2nd plot
# This is the same as doing 'fig, (top_ax, bot_ax) = plt.subplots(2)'
# Histogram
weights = np.ones_like(histogram_data) / histogram_data.shape[0]
hist, bins = np.histogram(histogram_data, bins=50, weights=weights)
width = 0.7 * (bins[1] - bins[0])
center = (bins[:-1] + bins[1:]) / 2
# Use top_ax to modify anything with the histogram plot
top_ax.bar(center, hist, align='center', width=width)
# ax.text(x, y, str). Make sure x,y are within your plot bounds ((0, 1), (0, .5))
top_ax.text(0.5, 0.5, "Here is text on the top plot", color='r')
# Heatmap
heatmap_params = {'cmap':plt.cm.Blues, 'alpha':0.8, 'vmin':0, 'vmax':1}
# Use bot_ax to modify anything with the heatmap plot
heatmap = bot_ax.pcolor(heatmap_data, **heatmap_params)
cbar = fig.colorbar(heatmap, shrink=0.8, aspect=10, fraction=.1,pad=.01)
# See how it looks
plt.show()

Grid Lines below the contour in Matplotlib

I have one question about the grid lines matplotlib.
I am not sure if this is possible to do or not.
I am plotting the following graph as shown in the image.
I won't give the entire code, since it is involving reading of files.
However the important part of code is here -
X, Y = np.meshgrid(smallX, smallY)
Z = np.zeros((len(X),len(X[0])))
plt.contourf(X, Y, Z, levels, cmap=cm.gray_r, zorder = 1)
plt.colorbar()
...
# Set Border width zero
[i.set_linewidth(0) for i in ax.spines.itervalues()]
gridLineWidth=0.1
ax.set_axisbelow(False)
gridlines = ax.get_xgridlines()+ax.get_ygridlines()
#ax.set_axisbelow(True)
plt.setp(gridlines, 'zorder', 5)
ax.yaxis.grid(True, linewidth=gridLineWidth, linestyle='-', color='0.6')
ax.xaxis.grid(False)
ax.xaxis.set_ticks_position('none')
ax.yaxis.set_ticks_position('none')
Now, my questions is like this -
If I put the grid lines below the contour, they disappear since they are below it.
If I put the grid line above the contour, they looks like what they are looking now.
However, what I would like to have is the grid lines should be visible, but should be below the black portion of the contour. I am not sure if that is possible.
Thank You !

In addition to specifying the z-order of the contours and the gridlines, you could also try masking the zero values of your contoured data.
Here's a small example:
import numpy as np
import matplotlib.pyplot as plt
x = np.arange(-2*np.pi, 2*np.pi, 0.1)
y = np.arange(-2*np.pi, 2*np.pi, 0.1)
X, Y = np.meshgrid(x, y)
Z = np.sin(X) - np.cos(Y)
Z = np.ma.masked_less(Z, 0) # you use mask_equal(yourData, yourMagicValue)
fig, ax = plt.subplots()
ax.contourf(Z, zorder=5, cmap=plt.cm.coolwarm)
ax.xaxis.grid(True, zorder=0)
ax.yaxis.grid(True, zorder=0)
And the output: