I want to have a figure consisting of, let's say, four subplots. Two of them are usual line-plots, two of them imshow-images.
I can format the imshow-images to proper plots itself, because every single one of them needs its own colorbar, a modified axis and the other axis removed.
This, however, seems to be absolutely useless for the subplotting. Can anyone help me with that?
I use this for displaying the data of the "regular" plots above as a colormap (by scaling the input-array i to [ i, i, i, i, i, i ] for 2D and calling imshow() with it).
The following code first displays what I need as a subplot and the second one shows all I can do, which is not sufficient.
#!/usr/bin/env python
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
s = { 't':1, 'x':[1,2,3,4,5,6,7,8], 'D':[0.3,0.5,0.2,0.3,0.5,0.5,0.3,0.4] }
width = 40
# how I do it in just one plot
tot = []
for i in range(width):
tot.append(s['D'])
plt.imshow(tot, norm=LogNorm(vmin=0.001, vmax=1))
plt.colorbar()
plt.axes().axes.get_xaxis().set_visible(False)
plt.yticks([0, 2, 4, 6], [s['x'][0], s['x'][2], s['x'][4], s['x'][6]])
plt.show()
f = plt.figure(figsize=(20,20))
plt.subplot(211)
plt.plot(s['x'], s['D'])
plt.ylim([0, 1])
#colorplot
sp = f.add_subplot(212)
#reshape (just necessary to see something)
tot = []
for i in range(width):
tot.append(s['D'])
sp.imshow(tot, norm=LogNorm(vmin=0.001, vmax=1))
#what I can't do now but needs to be done:
#sp.colorbar()
#sp.axes().axes.get_xaxis().set_visible(False)
#sp.yticks([0, 200, 400, 600, 800, 1000], [s['x'][0], s['x'][200], s['x'][400], s['x'][600], s['x'][800], s['x'][1000]])
plt.show()
You can make use of matplotlibs object oriented interface rather than the state-machine interace in order to get better control over each axes. Also, to get control over the height/width of the colorbar you can make use of the AxesGrid toolkit of matplotlib.
For example:
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.colors import LogNorm
from matplotlib.ticker import MultipleLocator
s = {'t': 1,
'x': [1, 2, 3, 4, 5, 6, 7, 8],
'T': [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8],
'D': [0.3, 0.5, 0.2, 0.3, 0.5, 0.5, 0.3, 0.4]}
width = 40
tot = np.repeat(s['D'],width).reshape(len(s['D']), width)
tot2 = np.repeat(s['T'],width).reshape(len(s['D']), width)
fig, (ax1, ax2, ax3, ax4) = plt.subplots(1,4)
fig.suptitle('Title of figure', fontsize=20)
# Line plots
ax1.set_title('Title of ax1')
ax1.plot(s['x'], s['T'])
ax1.set_ylim(0,1)
ax2.set_title('Title of ax2')
ax2.plot(s['x'], s['D'])
# Set locations of ticks on y-axis (at every multiple of 0.25)
ax2.yaxis.set_major_locator(MultipleLocator(0.25))
# Set locations of ticks on x-axis (at every multiple of 2)
ax2.xaxis.set_major_locator(MultipleLocator(2))
ax2.set_ylim(0,1)
ax3.set_title('Title of ax3')
# Display image, `aspect='auto'` makes it fill the whole `axes` (ax3)
im3 = ax3.imshow(tot, norm=LogNorm(vmin=0.001, vmax=1), aspect='auto')
# Create divider for existing axes instance
divider3 = make_axes_locatable(ax3)
# Append axes to the right of ax3, with 20% width of ax3
cax3 = divider3.append_axes("right", size="20%", pad=0.05)
# Create colorbar in the appended axes
# Tick locations can be set with the kwarg `ticks`
# and the format of the ticklabels with kwarg `format`
cbar3 = plt.colorbar(im3, cax=cax3, ticks=MultipleLocator(0.2), format="%.2f")
# Remove xticks from ax3
ax3.xaxis.set_visible(False)
# Manually set ticklocations
ax3.set_yticks([0.0, 2.5, 3.14, 4.0, 5.2, 7.0])
ax4.set_title('Title of ax4')
im4 = ax4.imshow(tot2, norm=LogNorm(vmin=0.001, vmax=1), aspect='auto')
divider4 = make_axes_locatable(ax4)
cax4 = divider4.append_axes("right", size="20%", pad=0.05)
cbar4 = plt.colorbar(im4, cax=cax4)
ax4.xaxis.set_visible(False)
# Manually set ticklabels (not ticklocations, they remain unchanged)
ax4.set_yticklabels([0, 50, 30, 'foo', 'bar', 'baz'])
plt.tight_layout()
# Make space for title
plt.subplots_adjust(top=0.85)
plt.show()
You can change the locations and labels of the ticks on either axis with the set_ticks and set_ticklabels methods as in the example above.
As for what the make_axes_locatable function does, from the matplotlib site about the AxesGrid toolkit:
The axes_divider module provides a helper function
make_axes_locatable, which can be useful. It takes a existing axes
instance and create a divider for it.
ax = subplot(1,1,1)
divider = make_axes_locatable(ax)
make_axes_locatable returns an instance of the AxesLocator class,
derived from the Locator. It provides append_axes method that creates
a new axes on the given side of (“top”, “right”, “bottom” and “left”)
of the original axes.
Related
I would like to create sth like the following graph in matplotlib:
I have x = [0, 1, ..., 10], and for each x I have values from range [0, 60]. Lets say that the black line is the quantile of values for a given i from range x. For selected i I want to add horizontally histogram (with parameter density = True) like in the picture with the possibility to control the width of this histogram (in the picture it goes from 2 to 5 but I would like to set fixed width). How can I do that?
Yes, this is relatively straightforward with inset_axes:
import matplotlib.pyplot as plt
import numpy as np
fig, ax = plt.subplots()
x = np.random.randn(100)
ax.plot(x)
ylim = ax.get_ylim()
histax = ax.inset_axes([0.3, 0, 0.2, 1], transform=ax.transAxes)
histax.hist(x, orientation='horizontal', alpha=0.5 )
histax.set_facecolor('none')
histax.set_ylim(ylim)
plt.show()
You will probably want to clean up the axes etc, but that is the general idea.
I am plotting a convergence graph and to show deviations from the mean I am using connected boxplots:
For some reason Matplotlib forces ticks for each boxplot and I cannot seem to get them removed. My code for the current plot looks something like this:
label = ["" for i in range(160)]
no_labels = int(np.floor(len(label)/20))
for i in range(no_labels):
label[i*20] = str(i*no_samples/no_labels)
# Weird behaviour for the last label so adding it manually
label[-1] = no_samples
fig = plt.figure(figsize=(10,5))
ax = fig.add_axes([0,0,1,1])
ax.set_xlabel("Samples", labelpad=10)
ax.set_ylabel("Error (MSE)", labelpad=10)
ax.set_ylim(0, 0.11)
ax.boxplot(data, flierprops=flyprops, showcaps=False,
boxprops=colorprops, whiskerprops={'color' : 'tab:blue'},
labels=label, patch_artist=True)
I have tried multiple ways of manipulating axis ticks which are available in MPL.
1) Trying to let MPL do the work:
ax.xaxis.set_major_locator(MultipleLocator(20))
2) Trying to set ticks manually: ax.set_xticks([list_of_ticks])
3) Tried a workaround
ax.xaxis.set_minor_locator(MultipleLocator(20))
# Removing major ticks, setting minor ticks
ax.xaxis.set_tick_params(which='major', size=0, width=2, direction='in')
ax.yaxis.set_tick_params(which='major', size=5, width=2, direction='in')
None of these seemed to work and I am unsure why. I think it may have something to do with my label variable but if I don't include it in this way MPL with include an axis lable for every entry which is a mess.
How can I set axis ticks once every 1000 entries in a connected boxplots figure?`
Edit: The input data is a numpy array of shape (15, 160) s.t. there are 160 boxplots plotted of 15 samples each. Example data for 5 boxplots of 3 samples each would look like:
np.random.rand(3,5)
>>> array([[0.05942481, 0.03408175, 0.84021109, 0.27531937, 0.62428798],
[0.24658313, 0.77910387, 0.2161348 , 0.39101172, 0.14038211],
[0.40694432, 0.22979738, 0.87056873, 0.788295 , 0.29337562]])
The main issue seems to be that the ticks need to be updated after drawing the main plot, never before.
(Having ax = fig.add_axes([0, 0, 1, 1]) is also quite unusual to work with. The standard way is fig, ax = plt.subplots(figsize=(10, 5)) which lets matplotlib a bit of flexibility for the whitespace around the plot.)
The code of the question has some missing variables and data, but the following toy example should create something similar:
import numpy as np
import matplotlib.pyplot as plt
no_samples = 8000
x = np.linspace(0, no_samples, 160)
no_labels = int(np.floor(len(x) / 20))
label = [f'{i * no_samples / no_labels:.0f}' for i in range(no_labels+1)]
fig = plt.figure(figsize=(10, 5))
ax = fig.add_axes([0.1, 0.1, 0.85, 0.85])
N = 100
data = np.random.normal(np.tile(100 / (x+1000), N), 0.001).reshape(N, -1)
flyprops = {'markersize':0.01}
colorprops = None
ax.boxplot(data, flierprops=flyprops, showcaps=False,
boxprops=colorprops, whiskerprops={'color': 'tab:blue'},
patch_artist=True)
ax.set_xlabel("Samples", labelpad=10)
ax.set_ylabel("Error (MSE)", labelpad=10)
ax.set_ylim(0, 0.11)
ax.set_xticks(range(0, len(x)+1, 20))
ax.set_xticklabels(label)
plt.show()
Here is an example of setting the tick marks:
import matplotlib.pyplot as plt
import numpy as np
data=np.random.rand(3,50)
fig = plt.figure(figsize=(10,5))
ax = fig.add_axes([0,0,1,1])
ax.set_xlabel("Samples", labelpad=10)
ax.set_ylabel("Error (MSE)", labelpad=10)
ax.boxplot(data,
showcaps=False,
whiskerprops={'color' : 'tab:blue'},
patch_artist=True
)
plt.xticks([10, 20, 30, 40, 50],
["10", "20", "30", "40", "50"])
EDIT:
You can also avoid messing with strings and set the marks like this:
N=50
plt.xticks(np.linspace(0, N, num=6), np.linspace(0, N, num=6))
See here and this example.
Simple ticks can be acheived in a similar mannar as here (note data as transposed numpy array) using
import numpy as np
import matplotlib.pyplot as plt
data = np.array([ np.random.rand(100) for i in range(3) ]).T
plt.boxplot(data)
plt.xticks([1, 2, 3], ['mon', 'tue', 'wed'])
I am using the data present here to construct this heat map using seaborn and pandas.
Code:
import pandas
import seaborn.apionly as sns
# Read in csv file
df_trans = pandas.read_csv('LUH2_trans_matrix.csv')
sns.set(font_scale=0.8)
cmap = sns.cubehelix_palette(start=2.8, rot=.1, light=0.9, as_cmap=True)
cmap.set_under('gray') # 0 values in activity matrix are shown in gray (inactive transitions)
df_trans = df_trans.set_index(['Unnamed: 0'])
ax = sns.heatmap(df_trans, cmap=cmap, linewidths=.5, linecolor='lightgray')
# X - Y axis labels
ax.set_ylabel('FROM')
ax.set_xlabel('TO')
# Rotate tick labels
locs, labels = plt.xticks()
plt.setp(labels, rotation=0)
locs, labels = plt.yticks()
plt.setp(labels, rotation=0)
# revert matplotlib params
sns.reset_orig()
As you can see from csv file, it contains 3 discrete values: 0, -1 and 1. I want a discrete legend instead of the colorbar. Labeling 0 as A, -1 as B and 1 as C. How can I do that?
Well, there's definitely more than one way to accomplish this. In this case, with only three colors needed, I would pick the colors myself by creating a LinearSegmentedColormap instead of generating them with cubehelix_palette. If there were enough colors to warrant using cubehelix_palette, I would define the segments on colormap using the boundaries option of the cbar_kws parameter. Either way, the ticks can be manually specified using set_ticks and set_ticklabels.
The following code sample demonstrates the manual creation of LinearSegmentedColormap, and includes comments on how to specify boundaries if using a cubehelix_palette instead.
import matplotlib.pyplot as plt
import pandas
import seaborn.apionly as sns
from matplotlib.colors import LinearSegmentedColormap
sns.set(font_scale=0.8)
dataFrame = pandas.read_csv('LUH2_trans_matrix.csv').set_index(['Unnamed: 0'])
# For only three colors, it's easier to choose them yourself.
# If you still really want to generate a colormap with cubehelix_palette instead,
# add a cbar_kws={"boundaries": linspace(-1, 1, 4)} to the heatmap invocation
# to have it generate a discrete colorbar instead of a continous one.
myColors = ((0.8, 0.0, 0.0, 1.0), (0.0, 0.8, 0.0, 1.0), (0.0, 0.0, 0.8, 1.0))
cmap = LinearSegmentedColormap.from_list('Custom', myColors, len(myColors))
ax = sns.heatmap(dataFrame, cmap=cmap, linewidths=.5, linecolor='lightgray')
# Manually specify colorbar labelling after it's been generated
colorbar = ax.collections[0].colorbar
colorbar.set_ticks([-0.667, 0, 0.667])
colorbar.set_ticklabels(['B', 'A', 'C'])
# X - Y axis labels
ax.set_ylabel('FROM')
ax.set_xlabel('TO')
# Only y-axis labels need their rotation set, x-axis labels already have a rotation of 0
_, labels = plt.yticks()
plt.setp(labels, rotation=0)
plt.show()
Here's a simple solution based on the other answers that generalizes beyond 3 categories and uses a dict (vmap) to define the labels.
import seaborn as sns
import numpy as np
# This just makes some sample 2D data and a corresponding vmap dict with labels for the values in the data
data = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
vmap = {i: chr(65 + i) for i in range(len(np.ravel(data)))}
n = len(vmap)
print(vmap)
cmap = sns.color_palette("deep", n)
ax = sns.heatmap(data, cmap=cmap)
# Get the colorbar object from the Seaborn heatmap
colorbar = ax.collections[0].colorbar
# The list comprehension calculates the positions to place the labels to be evenly distributed across the colorbar
r = colorbar.vmax - colorbar.vmin
colorbar.set_ticks([colorbar.vmin + 0.5 * r / (n) + r * i / (n) for i in range(n)])
colorbar.set_ticklabels(list(vmap.values()))
I find that a discretized colorbar in seaborn is much easier to create if you use a ListedColormap. There's no need to define your own functions, just add a few lines to basically customize your axes.
import pandas
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib.colors import ListedColormap
# Read in csv file
df_trans = pandas.read_csv('LUH2_trans_matrix.csv')
sns.set(font_scale=0.8)
# cmap is now a list of colors
cmap = sns.cubehelix_palette(start=2.8, rot=.1, light=0.9, n_colors=3)
df_trans = df_trans.set_index(['Unnamed: 0'])
# Create two appropriately sized subplots
grid_kws = {'width_ratios': (0.9, 0.03), 'wspace': 0.18}
fig, (ax, cbar_ax) = plt.subplots(1, 2, gridspec_kw=grid_kws)
ax = sns.heatmap(df_trans, ax=ax, cbar_ax=cbar_ax, cmap=ListedColormap(cmap),
linewidths=.5, linecolor='lightgray',
cbar_kws={'orientation': 'vertical'})
# Customize tick marks and positions
cbar_ax.set_yticklabels(['B', 'A', 'C'])
cbar_ax.yaxis.set_ticks([ 0.16666667, 0.5, 0.83333333])
# X - Y axis labels
ax.set_ylabel('FROM')
ax.set_xlabel('TO')
# Rotate tick labels
locs, labels = plt.xticks()
plt.setp(labels, rotation=0)
locs, labels = plt.yticks()
plt.setp(labels, rotation=0)
The link provided by #Fabio Lamanna is a great start.
From there, you still want to set colorbar labels in the correct location and use tick labels that correspond to your data.
assuming that you have equally spaced levels in your data, this produces a nice discrete colorbar:
Basically, this comes down to turning off the seaborn colorbar and replacing it with a discretized colorbar yourself.
import pandas
import seaborn.apionly as sns
import matplotlib.pyplot as plt
import numpy as np
import matplotlib
def cmap_discretize(cmap, N):
"""Return a discrete colormap from the continuous colormap cmap.
cmap: colormap instance, eg. cm.jet.
N: number of colors.
Example
x = resize(arange(100), (5,100))
djet = cmap_discretize(cm.jet, 5)
imshow(x, cmap=djet)
"""
if type(cmap) == str:
cmap = plt.get_cmap(cmap)
colors_i = np.concatenate((np.linspace(0, 1., N), (0.,0.,0.,0.)))
colors_rgba = cmap(colors_i)
indices = np.linspace(0, 1., N+1)
cdict = {}
for ki,key in enumerate(('red','green','blue')):
cdict[key] = [ (indices[i], colors_rgba[i-1,ki], colors_rgba[i,ki]) for i in xrange(N+1) ]
# Return colormap object.
return matplotlib.colors.LinearSegmentedColormap(cmap.name + "_%d"%N, cdict, 1024)
def colorbar_index(ncolors, cmap, data):
"""Put the colorbar labels in the correct positions
using uique levels of data as tickLabels
"""
cmap = cmap_discretize(cmap, ncolors)
mappable = matplotlib.cm.ScalarMappable(cmap=cmap)
mappable.set_array([])
mappable.set_clim(-0.5, ncolors+0.5)
colorbar = plt.colorbar(mappable)
colorbar.set_ticks(np.linspace(0, ncolors, ncolors))
colorbar.set_ticklabels(np.unique(data))
# Read in csv file
df_trans = pandas.read_csv('d:/LUH2_trans_matrix.csv')
sns.set(font_scale=0.8)
cmap = sns.cubehelix_palette(n_colors=3,start=2.8, rot=.1, light=0.9, as_cmap=True)
cmap.set_under('gray') # 0 values in activity matrix are shown in gray (inactive transitions)
df_trans = df_trans.set_index(['Unnamed: 0'])
N = df_trans.max().max() - df_trans.min().min() + 1
f, ax = plt.subplots()
ax = sns.heatmap(df_trans, cmap=cmap, linewidths=.5, linecolor='lightgray',cbar=False)
colorbar_index(ncolors=N, cmap=cmap,data=df_trans)
# X - Y axis labels
ax.set_ylabel('FROM')
ax.set_xlabel('TO')
# Rotate tick labels
locs, labels = plt.xticks()
plt.setp(labels, rotation=0)
locs, labels = plt.yticks()
plt.setp(labels, rotation=0)
# revert matplotlib params
sns.reset_orig()
bits and pieces recycled and adapted from here and here
I have the following plot:
I would like to make the x-axis ticks more readable by rotating the ticks by ~40 degrees. So from:
plt.xticks(list(range(0, width)), list(df_100.columns), rotation='90', fontsize=16)
To:
plt.xticks(list(range(0, width)), list(df_100.columns), rotation='40', fontsize=16)
When I do this, though, I get some crazy spacing issues:
(ignore the change in color...)
What's causing this problem? How can I fix it? Here's a minimum working example:
import matplotlib.pyplot as plt
import numpy as np
# Z is your data set
N = 100
height = df_100.shape[0]
width = df_100.shape[1]
# Z = np.random.random((100, 29))
# G is a NxNx3 matrix
G = np.zeros((height,width,3))
# Where we set the RGB for each pixel
G[Z>0.5] = [1, 1, 1]
G[Z<0.5] = [0.25, 0.25, 0.25]
fig, ax = plt.subplots(figsize=(20, 10))
ax.imshow(G, interpolation='none')
ax.set_aspect('auto')
ax.grid(None)
ax.xaxis.tick_top()
plt.xticks(list(range(0, width)), list(df_100.columns), rotation='45', fontsize=16)
plt.yticks([0, df_100.shape[0] - 1], [1, df_100.shape[0]], fontsize=20)
plt.tight_layout()
plt.show()
If xticklabels are of the same length, you won't have this kind of problem. But given different length of labels, you can encounter this kind of problem. Because the default rotation is from the center of the xlabel string. So you can try to set the rotation anchor properly from
['right', 'center', 'left'].
ha = 'left' # or 'right'. Experiment with it.
ax.set_xticks(x) # set tick location
ax.set_xticklabels(xlabels, rotation=40, ha=ha) # rotate the labels with proper anchoring.
I would like to reduce the width of the boxes in the boxplot below. Here's my code, but it is not working:
bp = plt.boxplot(boxes, widths = 0.6, patch_artist = True)
From the documentation there is a widths option:
widths : array-like, default = 0.5
Either a scalar or a vector and sets the width of each box. The default is 0.5, or 0.15*(distance between extreme positions) if that is smaller.
Here is an example:
import numpy as np
import matplotlib.pyplot as plt
np.random.seed(937)
data = np.random.lognormal(size=(37, 4), mean=1.5, sigma=1.75)
labels = list('ABCD')
fs = 10 # fontsize
plt.boxplot(data, labels=labels, showfliers=False, widths=(1, 0.5, 1.2, 0.1))
plt.show()
Try working via the axes and see if it works:
fig = plt.figure()
ax = fig.add_subplot(111)
ax.boxplot(boxes, widths = 0.6, patch_artist = True)