I'd like to plot EEG data and get this result:
But I am stuck on how to display the x axis label and its xlim.
After reading other questions, which use set_visible(False), I cannot resolve my issue.
I write my code in order to be reproducible:
sfreq = 256
raw_data = np.random.rand(14, 1000 * sfreq)
duration = 10 # duration of the signal
start = 200 * sfreq
final = start + int(sfreq * duration)
channels = list(np.arange(1, len(channels) + 1 ))
fig, ax = plt.subplots(len(channels), 1, sharex=True, figsize=(10, 10))
for idx, node in enumerate(channels):
data = raw_data[idx, start:final]
times = np.arange(1, data.size + 1) / sfreq
ax[idx].plot(times, data, lw=1., ls='-', c='k')
ax[idx].axis('off') # to remove bounding subplot
ax[idx].set_yticks([]) # to remove values from y axis
ax[idx].text(-1, 0, node, fontsize=12) # write text
# plt.axis(True)
# plt.axes().get_xaxis().set_visible(True)
# plt.xlim([200, 220])
plt.xlabel('Time (seconds)', fontsize=12)
plt.tight_layout()
plt.show()
This is my result:
But I'd like this:
Here are some possible changes to the plot:
make the code more python by using zip instead of an index in the for loop
change the visibility of the "spines" (the lines surrounding the subplot) instead of use axis('off')
remove the padding (margins)
use the axes transform to position the text of the y-axis
...
import matplotlib.pyplot as plt
import numpy as np
sfreq = 256
raw_data = np.random.rand(14, 1000 * sfreq)
duration = 10 # duration of the signal
start = 200 * sfreq
final = start + int(sfreq * duration)
channels = np.arange(len(raw_data)) + 1
fig, axs = plt.subplots(len(channels), 1, sharex=True, figsize=(10, 10))
for ax, node, data in zip(axs, channels, raw_data):
data = data[start:final]
times = np.arange(1, data.size + 1) / sfreq
ax.plot(times, data, lw=1., ls='-', c='k')
ax.set_yticks([]) # remove y ticks
for sp in ax.spines:
ax.spines[sp].set_visible(False) # hide the 4 lines surrounding the subplot
ax.text(-0.01, 0.5, node, fontsize=12, ha='right', va='center', transform=ax.transAxes) # write text
ax.margins(x=0) # avoid the empty space left and right
if ax != axs[-1]:
# ax.tick_params(axis='x', length=0) # hide the tick marks
ax.tick_params(bottom=False) # no tick marks at the bottom
axs[-1].set_xlabel('Time (seconds)', fontsize=12, labelpad=-10) # use negative padding to get closer to the xaxis
axs[-1].set_xticks([0, duration])
axs[-1].set_xticklabels([start // sfreq, final // sfreq])
axs[-1].spines['bottom'].set_bounds([0, duration]) # only draw the spine between the two ticks
axs[-1].spines['bottom'].set_visible(True)
axs[-1].spines['bottom'].set_linewidth(2)
plt.tight_layout()
plt.show()
Related
I've seen numerous examples of 3D plots using matplotlib/seaborn in Python but can't seem to get what I'm looking for; I have 50 or so timeseries that I would like to plot cleanly as in the following example below but with the name of the series on the axis; as an example I've marked in Goog, IBM, GE, Pepsi etc. Appreciate any pointers or examples. Thank you,
Example PLOT Click Here Please
Matplotlib has very rich gallery. I found this, you can only plot it once instead of animation. And manually put y-axis legend wherever you want.
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
# Fixing random state for reproducibility
np.random.seed(19680801)
# Create new Figure with black background
fig = plt.figure(figsize=(12, 8))
# Add a subplot with no frame
ax = plt.subplot(111, frameon=False)
# Generate random data
data = np.random.uniform(0, 1, (64, 75))
X = np.linspace(-1, 1, data.shape[-1])
G = 1.5 * np.exp(-4 * X ** 2)
# Generate line plots
lines = []
for i in range(len(data)):
# Small reduction of the X extents to get a cheap perspective effect
xscale = 1 - i / 200.
# Same for linewidth (thicker strokes on bottom)
lw = 1.5 - i / 100.0
line, = ax.plot(xscale * X, i + G * data[i], color="b", lw=lw)
lines.append(line)
# Set y limit (or first line is cropped because of thickness)
ax.set_ylim(-1, 70)
# No ticks
ax.set_xticks([])
ax.set_yticks([])
# 2 part titles to get different font weights
ax.text(0.5, 1.0, "MATPLOTLIB ", transform=ax.transAxes,
ha="right", va="bottom", color="k",
family="sans-serif", fontweight="light", fontsize=16)
ax.text(0.5, 1.0, "UNCHAINED", transform=ax.transAxes,
ha="left", va="bottom", color="k",
family="sans-serif", fontweight="bold", fontsize=16)
def update(*args):
# Shift all data to the right
data[:, 1:] = data[:, :-1]
# Fill-in new values
data[:, 0] = np.random.uniform(0, 1, len(data))
# Update data
for i in range(len(data)):
lines[i].set_ydata(i + G * data[i])
# Return modified artists
return lines
# Construct the animation, using the update function as the animation director.
anim = animation.FuncAnimation(fig, update, interval=10)
plt.show()
images = wcs_request.get_data() # get image data
fig, axs = plt.subplots((len(images) + (6 - 1)) // 6, 6, figsize=(20, 20),
gridspec_kw={'hspace': 0.0, 'wspace': 0.0})
total = ((len(images) + (6 - 1)) // 6) * 6
for idx, (image, time) in enumerate(zip(images, wcs_request.get_dates())):
# Plot bbox
axs.flat[idx].imshow(image)
# Set title
axs.flat[idx].set_title(time.date().strftime("%d %B %Y"), fontsize=10, fontweight='bold')
# delete plots which have no data
for idx in range(len(images), total):
fig.delaxes(axs.flat[idx])
plt.suptitle(id, fontsize=12, fontweight='bold')
# fig.tight_layout(pad=0, h_pad=.1, w_pad=.1)
# fig.subplots_adjust(wspace=0, hspace=0)
plt.savefig(dir_out / f'{id}_map.png', dpi=300)
plt.close()
When I run the code above, I get a subplot with much larger vertical blank space than I want. How can I fix it? I already set wspace and hspace to 0.0
Well, there are many ways to generate a "nice" array of subplots; but assuming that your goal is to, e.g. create two rows of images where len(images)=10:
import matplotlib.pyplot as plt
images=range(10)
## assuming you want e.g. axes on your first row:
ncols = 6
# figure out how many plots will fall into the last row using modulo
ncols_last = (len(images) % ncols)
# and (if mod > 0 !) add one to the floor operation here:
nrows = (len(images) // ncols ) + (ncols_last > 0)
fig = plt.figure()
axes={}
for i in range(len(images)):
# note that for some reason, add_subplot() counts from 1, hence we use i+1 here
axes[i] = fig.add_subplot(nrows,ncols,i+1)
# add some content
for i,ax in axes.items():
ax.text(0,0,i)
ax.set_xlim(-1,1)
ax.set_ylim(-1,1)
plt.show()
Which should give you 6 plots on the first row and 4 on the second. You should be able to add your plot content like this:
for idx, (image, time) in enumerate(zip(images, wcs_request.get_dates())):
# Plot bbox
axes[idx].imshow(image)
# Set title
axes[idx].set_title(time.date().strftime("%d %B %Y"), fontsize=10, fontweight='bold')
Or alternatively, using gridspec in order to get access to further layout options:
import matplotlib.pyplot as plt
from matplotlib import gridspec
images=range(10)
ncols = 6
ncols_last = (len(images) % ncols)
nrows = (len(images) // ncols ) + (ncols_last > 0)
fig = plt.figure()
axes = {}
gs = gridspec.GridSpec(nrows, ncols,
left=0.1,right=.9,
bottom=0.1,top=.9,
wspace=0.25,hspace=0.3,
)
for i,(r,c) in enumerate([(r,c) for r in range(nrows) for c in range(ncols)]):
if i < len(images):
print(f"axes[{i}]: relates to the gridspec at index ({r},{c})")
axes[i] = fig.add_subplot(gs[r,c])
for i,ax in axes.items():
ax.text(0,0,i)
ax.set_xlim(-1,1)
ax.set_ylim(-1,1)
plt.show()
You may want to check out subplots_adjust, which let you specify:
The height of the padding between subplots, as a fraction of the average axes height.
fig, axs = plt.subplots(2,1)
fig.subplots_adjust(hspace=0.0)
So with hspace=0 there is no spacing at all:
I am not sure as to why this happens. Maybe it is just a simple mistake that I cannot see, but by using this code:
for filename in glob.glob('/Users/jacob/Desktop/MERS/new/NOT COAL/gensets/statistics_per_lgu/per_lgu_files/*.csv'):
base = os.path.basename(filename)
name = os.path.splitext(base)[0]
df = pd.read_csv(filename)
# Show 4 different binwidths
for i, binwidth in enumerate([10, 20, 30, 40]):
# Set up the plot
ax = plt.subplot(2, 2, i + 1)
plt.subplots_adjust( wspace=0.5, hspace=0.5)
# Draw the plot
ax.hist(df['New Capacity based on 0.8 PF'], bins=binwidth,
color='red', edgecolor='black',alpha=0.5)
# Title and labels
ax.set_title('Histogram with Binwidth = %d' % binwidth, size=10)
ax.set_xlabel('Capacity', size=11)
ax.set_ylabel('Frequency count', size=11)
ax.axvline(x=df['New Capacity based on 0.8 PF'].median(), linestyle='dashed', alpha=0.3, color='blue')
min_ylim, max_ylim = plt.ylim()
ax.text(x=df['New Capacity based on 0.8 PF'].median(),y= max_ylim*0.9, s='Median', alpha=0.7, color='blue',fontsize = 12)
ax.axvline(x=df['New Capacity based on 0.8 PF'].mean(), linestyle='dashed', alpha=0.9, color='green')
min_ylim, max_ylim = plt.ylim()
ax.text(x=df['New Capacity based on 0.8 PF'].mean(),y= max_ylim*0.5, s='Mean', alpha=0.9, color='green',fontsize = 12)
plt.tight_layout()
plt.grid(True)
plt.savefig('/Users/jacob/Documents/Gensets_gis/historgrams/per_lgu_files/{}.png'.format(name))
I get all files created like this attached photo here.
Any ideas as to what I've done wrong?
Thanks in advance.
attached photo of one histogram output
My desired result would be something like this.
Desired output
It doesn't create new subplots but it use previous ones and then it draw new plots on old plots so you have to use clear subplot before you draw new histogram.
ax = plt.subplot(2, 2, i + 1)
ax.clear()
Example code. It gives desired output but if you remove `ax.clear() then first image will be OK but you get new plot with old plots on second and third image.
import os
import pandas as pd
import matplotlib.pyplot as plt
import random
for n in range(3):
filename = f'example_data_{n}.csv'
base = os.path.basename(filename)
name = os.path.splitext(base)[0]
df = pd.DataFrame({'New Capacity based on 0.8 PF': random.choices(list(range(1000)), k=100)})
data = df['New Capacity based on 0.8 PF']
median = data.median()
mean = data.mean()
# Show 4 different binwidths
for i, binwidth in enumerate([10, 20, 30, 40]):
# Set up the plot
ax = plt.subplot(2,2,i+1)
ax.clear() # <--- it removes previous histogram
plt.subplots_adjust( wspace=0.5, hspace=0.5)
# Draw the plot
ax.hist(data , bins=binwidth, color='red', edgecolor='black',alpha=0.5)
# Title and labels
ax.set_title('Histogram with Binwidth = %d' % binwidth, size=10)
ax.set_xlabel('Capacity', size=11)
ax.set_ylabel('Frequency count', size=11)
min_ylim, max_ylim = plt.ylim()
ax.axvline(x=median, linestyle='dashed', alpha=0.3, color='blue')
ax.text(x=median, y= max_ylim*0.9, s='Median', alpha=0.7, color='blue',fontsize = 12)
ax.axvline(x=mean, linestyle='dashed', alpha=0.9, color='green')
ax.text(x=mean, y= max_ylim*0.5, s='Mean', alpha=0.9, color='green',fontsize = 12)
plt.tight_layout()
plt.grid(True)
plt.savefig('{}.png'.format(name))
i have a little problem to create a subplot loop.
The following code show my result for one plot.... So it starts with a dayloop than with a hour loop (8 timesteps).
If i run the code i get a nice QUiver plot with the colorbar.
for dd in range(1,15):
day=str(dd)
readfile=fns[files_indizes[dd]]
if dd < 10:
nc_u_comp = NetCDFFile(ROOT+u_comp1+'0'+day+comp)
nc_v_comp = NetCDFFile(ROOT+v_comp1+'0'+day+comp)
else:
nc_u_comp = NetCDFFile(ROOT+u_comp1+day+comp)
nc_v_comp = NetCDFFile(ROOT+v_comp1+day+comp)
time = nc_u_comp.variables['time'][:]
index=readfile.find(comp)
index=index+len(comp)
date=readfile[index-14:index-6]
plt.clf()
for tt in range(0,len(time)):
if tt < 10:
h =str(0)+str(tt)
else:
h=str(tt)
varU=nc_u_comp.variables['u10'][tt,:,:]
varV=nc_v_comp.variables['v10'][tt,:,:]
lat = nc_u_comp.variables['latitude'][:]
lon = nc_u_comp.variables['longitude'][:]
plt.rcParams["figure.figsize"] = [10,10]
#plane projection of the world
#map with box size (defintion on the top)
box = sgeom.box(minx=llcrnrlon, maxx=urcrnrlon, miny=llcrnrlat, maxy=urcrnrlat)
x0, y0, x1, y1 = box.bounds
#Map plot. The middel of the map is central_longitude
#proj = ccrs.PlateCarree(central_longitude=0)
proj=ccrs.PlateCarree()
#Change middelpoint of the map
box_proj = ccrs.PlateCarree(central_longitude=0)
ax2 = plt.axes(projection=proj)
ax2.set_extent([x0, x1, y0, y1], box_proj)
ax2.add_feature(cartopy.feature.BORDERS, linestyle='-', alpha=.5)
ax2.coastlines(resolution='50m')
#Definition of the scale_bar
gl = ax2.gridlines(ccrs.PlateCarree(), \
linestyle='--', alpha=1, linewidth=0.5, draw_labels=True)
gl.xlabels_top = False
gl.ylabels_right = False
gl.xformatter = LONGITUDE_FORMATTER
gl.yformatter = LATITUDE_FORMATTER
magnitude = (varU ** 2 + varV ** 2) ** 0.5
strm =plt.streamplot(lon , lat , varU, varV, linewidth=2, density=2, color=magnitude)
cbar= plt.colorbar()
cbar.set_label('$m/s$')
name='Wind in 10 m '+ date + h+' UTC'
ax2.set_aspect('auto')
plt.title(name, y=1)
Now i want to create an 2x4 Subplot array with a colorbar allocate to the complete Subplot array.
I find some infromation in the internet, but it doesn't run with my code. Maybe someone can help me?
This shows how to plot an array of simple Cartopy maps in 4 rows 2 columns. Also shows how to plot a colorbar to accompany the maps array. Hope it helps.
import numpy as np
import cartopy.crs as ccrs
import matplotlib.pyplot as plt
import matplotlib as mpl
# create figure with figsize big enough to accomodate all maps, labels, etc.
fig = plt.figure(figsize=(8, 10), tight_layout=False)
# define plot array's arrangement
columns = 2
rows = 4
# set projection to use
projex = ccrs.PlateCarree()
# set the colormap and norm for
# the colorbar to use
cmap1 = mpl.cm.magma
norm1 = mpl.colors.Normalize(vmin=0, vmax=100)
def plotmymap(axs):
# your plot specs of each map should replace this
img = np.random.randint(100, size=(15, 30)) # 2d array of random values (1-100)
# render image on current axis
plims = plt.imshow(img, extent=[-180,180,-90,90], alpha=0.5, cmap=cmap1, norm=norm1)
axs.set_global()
axs.coastlines()
# add title to the map
axs.set_title("Map_"+str(i))
return plims # for use by colorbar
for i in range(1, columns*rows +1):
# add a subplot into the array of plots
ax = fig.add_subplot(rows, columns, i, projection=projex)
plims = plotmymap(ax) # a simple maps is created on subplot
# add a subplot for vertical colorbar
bottom, top = 0.1, 0.9
left, right = 0.1, 0.8
fig.subplots_adjust(top=top, bottom=bottom, left=left, right=right, hspace=0.15, wspace=0.25)
cbar_ax = fig.add_axes([0.85, bottom, 0.05, top-bottom])
fig.colorbar(plims, cax=cbar_ax) # plot colorbar
plt.show() # this plot all the maps
The resulting plots:
I just created a horizontal stacked bar chart using matplotlib, and I can't figure out why there is extra space between the x axis and the first bar (code and picture below). Any suggestions or questions? Thanks!
Code:
fig = figure(facecolor="white")
ax1 = fig.add_subplot(111, axisbg="white")
heights = .43
data = np.array([source['loan1'],source['loan2'],source['loan3']])
dat2 = np.array(source2)
ind=np.arange(N)
left = np.vstack((np.zeros((data.shape[1],), dtype=data.dtype), np.cumsum(data, axis=0) [:-1]))
colors = ( '#27A545', '#7D3CBD', '#C72121')
for dat, col, lefts, pname2 in zip(data, colors, left, pname):
ax1.barh(ind+(heights/2), dat, color=col, left=lefts, height = heights, align='center', alpha = .5)
p4 = ax1.barh(ind-(heights/2), dat2, height=heights, color = "#C6C6C6", align='center', alpha = .7)
ax1.spines['right'].set_visible(False)
ax1.yaxis.set_ticks_position('left')
ax1.spines['top'].set_visible(False)
ax1.xaxis.set_ticks_position('bottom')
yticks([z for z in range(N)], namelist)
#mostly for the legend
params = {'legend.fontsize': 8}
rcParams.update(params)
box = ax1.get_position()
ax1.set_position([box.x0, box.y0 + box.height * 0.1, box.width, box.height * 0.9])
l = ax1.legend(loc = 'upper center', bbox_to_anchor=(0.5,-0.05), fancybox=True, shadow = True, ncol = 4)
show()
This is because matplotlib tries to intelligently choose minimum and maximum limits for the plot (i.e. "round-ish" numbers) by default.
This makes a lot of sense for some plots, but not for others.
To disable it, just do ax.axis('tight') to snap the data limits to the strict extents of the data.
If you want a bit of padding despite the "tight" bounds on the axes limits, use ax.margins.
In your case, you'd probably want something like:
# 5% padding on the y-axis and none on the x-axis
ax.margins(0, 0.05)
# Snap to data limits (with padding specified above)
ax.axis('tight')
Also, if you want to set the extents manually, you can just do
ax.axis([xmin, xmax, ymin, ymax])`
or use set_xlim, set_ylim, or even
ax.set(xlim=[xmin, xmax], ylim=[ymin, ymax], title='blah', xlabel='etc')