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I am creating a 2D matplotlib plot (i and j coordinates) which contains 10 subplots. Each subplot contains 150 by 150 grid cell data. How can I insert a small black-colored square mark (3 by 3 ) somewhere fixed (center at coordinates 62 and 62 ) on each generated heatmap sub-plot across those 10 sub-plots? The square mark would therefore contain 10 blocks from 60 to 64 in both x and y direction and contains a written text "Sale 1" centered at x 62 and y 62. My code below does not generate any patches. Any feedback is greatly appreciated.
from matplotlib.patches import Rectangle
import numpy as np
import matplotlib.pyplot as plt
from sklearn.metrics import r2_score, median_absolute_error
import os
import matplotlib.cm as cm
from mpl_toolkits import axes_grid1
import matplotlib.pyplot as plt
#import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib.colors as mcolors
import matplotlib.colors
import matplotlib.colors as colors
data = np.random.rand(10, 150, 150)
data = data.reshape(-1, 1)
property = "Sale"
pmin = data.min()
pmax = data.max()
v = np.linspace(round(pmin,3), round(pmax,3),15, endpoint=True)
v = [round(x,3) for x in v]
fig, ax = plt.subplots(2, 5, figsize=(160, 80))
row_count = 0
col_count = 0
for i in range(10):
sub_plot_data = data[(i)*(150*150):(i+1)*150*150]
x = 150
y = 150
#--------------------------- Define the map boundary ----------------------
xmin = 1258096.6
xmax = 1291155.0
ymin = 11251941.6
ymax = 11285000.0
pmin = min(sub_plot_data)
pmax = max(sub_plot_data)
# --------------------------- define color bar for Discrete color
bounds = np.linspace(-1, 1, 10)
Discrete_colors = plt.get_cmap('jet')(np.linspace(0,1,len(bounds)+1))
# create colormap without the outmost colors
cmap = mcolors.ListedColormap(Discrete_colors[1:-1]) #
actual_2d = np.reshape(sub_plot_data,(y,x))
im1 = ax[row_count, col_count].imshow(actual_2d, interpolation=None, cmap=cmap,
extent=(xmin, xmax, ymin, ymax), vmin=pmin, vmax=pmax)
plt.text(actual_2d[62, 62], actual_2d[62, 62], '%s' % 'Sale_1',
horizontalalignment='center', verticalalignment='center', color= 'black', fontsize= 90)
ax[row_count, col_count].set_title("Sale_Stores-%s - L: %s"%(i+1, layer),
fontsize=130, pad=44, x=0.5, y=0.999) # new
ax[row_count, col_count].set_aspect('auto')
ax[row_count, col_count].tick_params(left=False, labelleft=False, top=False,
labeltop=False, right=False, labelright=False, bottom=False, labelbottom=False) # new
#ax[row_count, col_count] = plt.gca()
plt.gca().add_patch(Rectangle((60, 60), 3, 3, edgecolor='black',
facecolor='black',fill=True,lw=2))
ax[row_count, col_count].add_patch(plt.text(62, 62, '%s' % 'Sale_1',
horizontalalignment='center', verticalalignment='center', color= 'black', fontsize= 90))
col_count +=1
if col_count == 5:
row_count +=1
col_count =0
fig.tight_layout(h_pad=10)
plt.subplots_adjust(left=0.02,
bottom=0.1,
right=0.91,
top=0.8,
wspace=0.1,
hspace=0.2)
cbaxes = fig.add_axes([0.94, 0.05, 0.02, 0.8])
cbar = fig.colorbar(im1, ax=ax.ravel().tolist(), ticks=v, extend='both', cax =cbaxes)
cbar.ax.tick_params(labelsize=70)
#cbar.set_ticks(v)
cbar.ax.set_yticklabels([i for i in v], fontsize=120)
output_dir = r"D/test"
plot_dir = os.path.join(output_dir, reservoir_property)
if not os.path.exists(plot_dir):
os.makedirs(plot_dir)
fig.savefig(r"%s/per_allmodel.png"%(plot_dir))
I tried your code and made a couple of modifications: first, the graph size was too huge and caused errors, so I made it smaller; second, I simplified the subplots: axes has a list of subplot objects, so I took them out with axes.flat; third The second is modifying the text as annotations. The graph size has been reduced and the font size and spacing have been adjusted, so please modify it yourself. Finally, tick_params is not set since the color bar ticks are disabled.
fig, axes = plt.subplots(2, 5, figsize=(16, 8))
row_count = 0
col_count = 0
for i,ax in enumerate(axes.flat):
sub_plot_data = data[(i)*(150*150):(i+1)*150*150]
x = 150
y = 150
#--------------------------- Define the map boundary ----------------------
xmin = 1258096.6
xmax = 1291155.0
ymin = 11251941.6
ymax = 11285000.0
pmin = min(sub_plot_data)
pmax = max(sub_plot_data)
# --------------------------- define color bar for Discrete color
bounds = np.linspace(-1, 1, 10)
Discrete_colors = plt.get_cmap('jet')(np.linspace(0,1,len(bounds)+1))
# create colormap without the outmost colors
cmap = mcolors.ListedColormap(Discrete_colors[1:-1]) #
actual_2d = np.reshape(sub_plot_data,(y,x))
#im = ax.imshow(actual_2d, interpolation=None, cmap=cmap, extent=(xmin, xmax, ymin, ymax), vmin=pmin, vmax=pmax)
im = ax.imshow(actual_2d, interpolation=None, cmap=cmap)
ax.text(actual_2d[62, 62], actual_2d[62, 62]-10, '%s' % 'Sale_1',
horizontalalignment='center', verticalalignment='center', color= 'black', fontsize=18)
ax.set_title("Sale_Stores-%s - L: %s"%(i+1, 1), fontsize=14, pad=30, x=0.5, y=0.999)
ax.set_aspect('auto')
ax.add_patch(Rectangle((60, 60), 6, 6, edgecolor='red', facecolor='red', fill=True, lw=2))
ax.text(62, 62, '%s' % 'Sale_1', ha='center', va='center', color='black', fontsize=14)
fig.tight_layout(h_pad=10)
plt.subplots_adjust(left=0.02,
bottom=0.1,
right=0.91,
top=0.8,
wspace=0.1,
hspace=0.5)
cbaxes = fig.add_axes([0.94, 0.05, 0.02, 0.8])
cbar = fig.colorbar(im, ax=axes.flat, ticks=v, extend='both', cax=cbaxes)
cbar.ax.tick_params(labelsize=10)
#cbar.set_ticks(v)
cbar.ax.set_yticklabels([str(i) for i in v], fontsize=12)
#plt.tick_params(left=False, labelleft=False, top=False, labeltop=False, right=False, labelright=False, bottom=False, labelbottom=False)
plt.show()
Im not sure if i use the wrong data or if there is and edit i need to do and not seeing it. It would be nice if someone could take a look at the code. The problem here is that yerr at the first bar is at x=0 and in the image the yerr is somewhere around 2.5
Does someone know what i did wrong or forgot to edit?
the end result should be:
my code:
import numpy as np
import matplotlib.pyplot as plt
np.random.seed(1)
y_raw = np.random.randn(1000).cumsum() + 15
x_raw = np.linspace(0, 24, y_raw.size)
x_pos = x_raw.reshape(-1, 100).min(axis=1)
y_avg = y_raw.reshape(-1, 100).mean(axis=1)
y_err = y_raw.reshape(-1, 100).ptp(axis=1)
bar_width = x_pos[1] - x_pos[0]
x_pred = np.linspace(0, 30)
y_max_pred = y_avg[0] + y_err[0] + 2.3 * x_pred
y_min_pred = y_avg[0] - y_err[0] + 1.2 * x_pred
barcolor, linecolor, fillcolor = 'wheat', 'salmon', 'lightblue'
fig, axes = fig, ax = plt.subplots()
axes.set_title(label="Future Projection of Attitudes", fontsize=15)
plt.xlabel('Minutes since class began', fontsize=12)
plt.ylabel('Snarkiness (snark units)', fontsize=12)
fig.set_size_inches(8, 6, forward=True)
axes.fill_between(x_pred, y_min_pred, y_max_pred ,color='lightblue')
axes.plot(x_raw, y_raw, color='salmon')
vert_bars = axes.bar(x_pos, y_avg, yerr=y_err, color='wheat', width = bar_width, edgecolor='grey',error_kw=dict(lw=1, capsize=5, capthick=1, ecolor='gray'))
axes.set(xlim=[0, 30], ylim=[0,100])
plt.show()
yerr is meant to be the difference between the mean and the min/max. Now you're using the full difference between max and min. You might divide it by 2 to get a better approximation. To obtain the exact values, you could calculate them explicitly (see code example).
Further, by default, the bars are center aligned vs their x-position. You can use align='edge' to left-align them (as x_pos is calculated as the minimum of the range the bar represents). You could also set clip_on=False in the err_kw to make sure the error bars are never clipped by the axes.
import numpy as np
import matplotlib.pyplot as plt
np.random.seed(1)
y_raw = np.random.randn(1000).cumsum() + 15
x_raw = np.linspace(0, 24, y_raw.size)
x_pos = x_raw.reshape(-1, 100).min(axis=1)
y_avg = y_raw.reshape(-1, 100).mean(axis=1)
y_min = y_raw.reshape(-1, 100).min(axis=1)
y_max = y_raw.reshape(-1, 100).max(axis=1)
bar_width = x_pos[1] - x_pos[0]
x_pred = np.linspace(0, 30)
y_max_pred = y_avg[0] + y_err[0] + 2.3 * x_pred
y_min_pred = y_avg[0] - y_err[0] + 1.2 * x_pred
barcolor, linecolor, fillcolor = 'wheat', 'salmon', 'lightblue'
fig, ax = plt.subplots(figsize=(8, 6))
ax.set_title(label="Future Projection of Attitudes", fontsize=15)
ax.set_xlabel('Minutes since class began', fontsize=12)
ax.set_ylabel('Snarkiness (snark units)', fontsize=12)
ax.fill_between(x_pred, y_min_pred, y_max_pred, color='lightblue')
ax.plot(x_raw, y_raw, color='salmon')
vert_bars = ax.bar(x_pos, y_avg, yerr=(y_avg - y_min, y_max - y_avg),
color='wheat', width=bar_width, edgecolor='grey', align='edge',
error_kw=dict(lw=1, capsize=5, capthick=1, ecolor='grey', clip_on=False))
ax.set(xlim=[0, 30], ylim=[0, 100])
plt.tight_layout()
plt.show()
I have been using Is it possible to get color gradients under curve in matplotlib? as a reference (you can see the similarities, however i cant for the life of me figure out how to push the shading all the way down to 0 on the Y AXIS, for some reason which i cant find out, it has an upward sloping straight line cutting off the shading, i cant find anything in my data to suggest why its doing this.
for context the y axis can show positive and negative and i want to fill the scale the whole way so using gradient colour to fill from 0 to the line (positive) then fill from 0 to the negative line (see my blue example from a previous chart -same data-)
Here is my code
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.colors as mcolors
from matplotlib.patches import Polygon
# Variables
AUM = df['#AHD_AUM'].head(104)
MM = df['#AHD_Managed_Money_Net'].head(104)
PRICE = df['#AHD_Price'].head(104)
DATES = df['DATES'].head(104)
# Date Friendly Variables for Plot
List_AUM = df['#AHD_AUM'].head(104).to_list()
List_MM = df['#AHD_Managed_Money_Net'].head(104).to_list()
List_DATES = df['DATES'].head(104).to_list()
X = 0 * df['#AHD_AUM'].head(104)
# Make a date list changing dates with numbers to avoid the issue with the plot
interpreting dates
for i in range(len(df['DATES'].head(104))):
count = i
df['count'][i] = 120 - i
# X and Y data variables changed to arrays as when i had these set as dates
matplotlib hates it
x = df['count'].head(104).to_numpy()
y = df['#AHD_Managed_Money_Net'].head(104).to_numpy()
#DD = AUM.to_numpy()
#MMM = MM.to_numpy()
def main():
for _ in range(len(DD)):
gradient_fill(x,y)
plt.show()
def gradient_fill(x,y, fill_color=None, ax=None, **kwargs):
"""
"""
if ax is None:
ax = plt.gca()
line, = ax.plot(x, y, **kwargs)
if fill_color is None:
fill_color = line.get_color()
zorder = line.get_zorder()
alpha = line.get_alpha()
alpha = 1.0 if alpha is None else alpha
z = np.empty((100, 1, 4), dtype=float)
rgb = mcolors.colorConverter.to_rgb(fill_color)
z[:,:,:3] = rgb
z[:,:,-1] = np.linspace(0, alpha, 100)[:,None]
xmin, xmax, ymin, ymax = x.min(), x.max(), y.min(), y.max()
im = ax.imshow(z, aspect='auto', extent=[xmin, xmax, ymin, ymax],
origin='lower', zorder=zorder)
xy = np.column_stack([x, y])
# xy = np.vstack([[xmin, ymin], xy, [xmax, ymin], [xmin, ymin]]) ### i dont
need this so i have just commented it out
clip_path = Polygon(xy, facecolor='none', edgecolor='none', closed=True)
ax.add_patch(clip_path)
im.set_clip_path(clip_path)
ax.autoscale(True)
return line, im
main()
this is my current output
An easier way to clip the gradient by the curve, is to use a polygon obtained from fill_between.
Here is some example code to get you started.
import numpy as np
import matplotlib.pyplot as plt
np.random.seed(123)
x = np.linspace(0, 10, 200)
y = np.random.normal(0.01, 1, 200).cumsum()
fig, ax = plt.subplots(figsize=(12, 5))
ax.plot(x, y)
ylim = ax.get_ylim()
grad1 = ax.imshow(np.linspace(0, 1, 256).reshape(-1, 1), cmap='Blues', vmin=-0.5, aspect='auto',
extent=[x.min(), x.max(), 0, y.max()], origin='lower')
poly_pos = ax.fill_between(x, y.min(), y, alpha=0.1)
grad1.set_clip_path(poly_pos.get_paths()[0], transform=ax.transData)
poly_pos.remove()
grad2 = ax.imshow(np.linspace(0, 1, 256).reshape(-1, 1), cmap='Reds', vmin=-0.5, aspect='auto',
extent=[x.min(), x.max(), y.min(), 0], origin='upper')
poly_neg = ax.fill_between(x, y, y.max(), alpha=0.1)
grad2.set_clip_path(poly_neg.get_paths()[0], transform=ax.transData)
poly_neg.remove()
ax.set_ylim(ylim)
ax.axhline(0, color='black') # show a line at x=0
plt.show()
PS: vmin in imshow can be used to remove the color range where it's very light:
grad1 = ax.imshow(np.linspace(0, 1, 256).reshape(-1, 1), cmap='Blues', vmin=-0.5, aspect='auto',
extent=[x.min(), x.max(), 0, y.max()], origin='lower')
grad2 = ax.imshow(np.linspace(0, 1, 256).reshape(-1, 1), cmap='Reds', vmin=-0.5, aspect='auto',
extent=[x.min(), x.max(), y.min(), 0], origin='upper')
import pandas as pd # For data handling
import seaborn as sns # For plotting
import numpy as np
import matplotlib.pyplot as plt # For plotting
import matplotlib
#some preferred user settings
plt.rcParams['figure.figsize'] = (18.0, 12.0)
pd.set_option('display.max_columns', None)
%matplotlib inline
import warnings
warnings.filterwarnings(action='ignore')
from mpl_toolkits.axisartist.parasite_axes import HostAxes, ParasiteAxes
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
import datetime as dt
import matplotlib.dates as mdates
import pandas
Metal = CAD
# Variables
AUM = Metal.iloc[:,[7]].head(104)
MM = Metal.iloc[:,[0]].head(104)
PRICE = Metal.iloc[:,[8]].head(104)
#Last_Report = Metal.iloc[:,[9]].head(1).dt.strftime('%d %b %Y').to_list()
DATES = Metal.iloc[:,[10]].head(104)
# Dataframe for Net Position High
Net_High = Metal[Metal.iloc[:,[0]] == Metal.iloc[:,[0]].max()]
# Variables for Chart Annotation for Net Position High
Pos_High_Date = Net_High.iloc[:, [0]]
Pos_High_AUM = Net_High.iloc[:, [7]][0]/[1000000000]
Pos_High_Price = Net_High.iloc[:, [8]].to_numpy()[0].round().astype('int')
Pos_High = Net_High.iloc[:, [0]][0].astype('int')
Str_Date = mdates.num2date(Pos_High_Date)
Str_Date = pd.to_datetime(Str_Date[0]).strftime("%d %b %y")[0]
# Dataframe for Net Position Low
Net_Low = df[df['#CAD_Managed_Money_Net'] == df['#CAD_Managed_Money_Net'].head(104).min()]
# Variables for Chart Annotation for Net Position High
Pos_Low_Date = Net_Low.iloc[:, [55]].to_numpy()
Pos_Low_AUM = Net_Low.iloc[:, [26]].to_numpy()[0].round()/[1000000000]
Pos_Low_Price = Net_Low.iloc[:, [27]].to_numpy()[0].round().astype('int')
Pos_Low = Net_Low['#CAD_Managed_Money_Net'][0].astype('int')
Str_Date_Low = mdates.num2date(Pos_Low_Date)
Str_Date_Low = pd.to_datetime(Str_Date_Low[0]).strftime("%d %b %y")[0]
# C Brand Colour Scheme
C = ['deepskyblue', '#003399', 'slategray', '#027608','#cc0000']
def make_patch_spines_invisible(ax):
ax.set_frame_on(True)
ax.patch.set_visible(False)
for sp in ax.spines.values():
sp.set_visible(False)
fig, host = plt.subplots(figsize=(25,15))
fig.subplots_adjust(right=0.8)
#twinx() creates another axes sharing the x axis we do this twice
par1 = host.twinx()
par2 = host.twinx()
# Offset the right spine of par2 the ticks
par2.spines["right"].set_position(("axes",1.08))
#because par2 was created by twinx the frame is off so we need to use the method created above
make_patch_spines_invisible(par2)
# second, show the right spine
par2.spines["right"].set_visible(True)
######### Colouring in Plots
x = DATES
y = MM
ylim = host.get_ylim()
Long = host.imshow(np.linspace(0, 1, 256).reshape(-1, 1), cmap= 'Blues', vmin=-0.5, aspect='auto',
extent=[x.min(), x.max(), 0, y.max()], origin='lower')
poly_pos = host.fill_between(x, y.min(), y, alpha=0.1)
Long.set_clip_path(poly_pos.get_paths()[0], transform=host.transData)
poly_pos.remove()
Short = host.imshow(np.linspace(0, 1, 256).reshape(-1, 1), cmap='OrRd', vmin=-0.5, aspect='auto',
extent=[x.min(), x.max(), y.min(), 0], origin='upper')
poly_neg = host.fill_between(x, y, y.max(), alpha=0.1)
Short.set_clip_path(poly_neg.get_paths()[0], transform=host.transData)
poly_neg.remove()
##########
#plot data
p1, = host.plot(DATES, MM, label="Managed Money Net Position", linewidth=0.0,color = Citi[1], alpha = 0.8)
p2, = par1.plot(DATES, AUM, label="AUM",linewidth=1, marker = '$A$',mew = 1,mfc = 'w', color = Citi[0], alpha = 0.8)
p3, = par2.plot(DATES, PRICE, label="3M Price",linewidth=1, marker = '$p$', color = Citi[2], alpha = 0.8)
#Automatically scale and format
host_labels = ['{:,.0f}'.format(x) + 'K Lots' for x in host.get_yticks()/1000]
host.set_yticklabels(host_labels)
par1_labels = ['{:,.1f}'.format(x) + ' $Billion' for x in par1.get_yticks()/1000000000]
par1.set_yticklabels(par1_labels)
par2_labels = ['{:,.0f}'.format(x) + ' $' for x in par2.get_yticks()]
par2.set_yticklabels(par2_labels)
# x Axis formatting (date)
formatter = matplotlib.dates.DateFormatter('%b- %Y')
host.xaxis.set_major_formatter(formatter)
# Rotates and right-aligns the x labels so they don't crowd each other.
for label in host.get_xticklabels(which='major'):
label.set(rotation=30, horizontalalignment='right')
# Axis Labels
host.set_xlabel("Date")
host.set_ylabel("Managed Money Net Position")
par1.set_ylabel("AUM")
par2.set_ylabel("3M Price")
# Tick Parameters
tkw = dict(size=10, width=2.5)
# Set tick colours
host.tick_params(axis = 'y', colors = Citi[1], **tkw)
par1.tick_params(axis = 'y', colors = Citi[0], **tkw)
par2.tick_params(axis = 'y', colors = Citi[2], **tkw)
#host.tick_params(which='major',axis = 'x',direction='out', colors = Citi[2], **tkw)
#plt.xticks(x, rotation='vertical')
#host.xaxis.set_major_locator(AutoMajorLocator())
host.xaxis.set_major_locator(MultipleLocator(24))
host.tick_params('x',which='major', length=7)
#Label colours taken from plot
host.yaxis.label.set_color(p1.get_color())
par1.yaxis.label.set_color(p2.get_color())
par2.yaxis.label.set_color(p3.get_color())
# Map Title
host.set_title('Aluminium Managed Money Net Positioning as of %s'% Last_Report[0],fontsize='large')
#Colour Spines cant figure out how to do it for the host
par1.spines["right"].set_edgecolor(p2.get_color())
par2.spines["right"].set_edgecolor(p3.get_color())
###### Annotation Tests ##########
## Net Position High Box
host.annotate(f' Net Position High | {Pos_High} \n Date | {Str_Date} \n AUM | ${Pos_High_AUM[0].round(1)} Billion\n 3M Price | ${Pos_High_Price[0]}$',
xy=(Pos_High_Date, Pos_High), xycoords='data',
xytext=(0.02, .85), textcoords='axes fraction',
horizontalalignment='left',
verticalalignment='bottom',
color='white',
bbox=dict(boxstyle="round", fc= Citi[1],edgecolor='white'),
arrowprops=dict(
facecolor='black',
arrowstyle= '->'))
## Net Position Low Box
host.annotate(f' Net Position Low | {Pos_Low} \n Date | {Str_Date_Low} \n AUM | ${Pos_Low_AUM[0].round(1)} Billion\n 3M Price | ${Pos_Low_Price[0]}$',
xy=(Pos_Low_Date, Pos_Low), xycoords='data',
xytext=(0.02, .80), textcoords='axes fraction',
horizontalalignment='left',
verticalalignment='top',
color='white',
bbox=dict(boxstyle="round", fc= Citi[4],edgecolor='white'),
arrowprops=dict(
facecolor='black',
arrowstyle= '->'))
################
# Legend - a little complicated as we have to take from multiple axis
lines = [p1, p2, p3]
########## Plot text and line on chart if you want to
# host.axvline(x = DATES[52] , linestyle='dotted', color='black') ###Dotted Line when Needed
# host.text(2020.3, 10, 'Managed Money \n Aluminium')
# host.text(2020.5, 92, r'Ali',color='black')
# host.text(2020.8,15, r'some event', rotation=90)
host.legend(lines,[l.get_label() for l in lines],loc=2, fontsize=12,frameon=False)
plt.savefig('multiple_axes.png', dpi=300, bbox_inches='tight')
I have a scatter plot of Lc and Fc values (please, refer to plot1).
Lc= [360.66832393 388.26294316 392.9410819 ... 384.31751584 403.52581547
384.22929343]
Fc= [77.3294787 47.5926941 44.53032575 ... 50.44012265 38.99666318
50.54763385]
plot.scatter(Lc, Fc)
I would like to draw the Fc profile of this scatter plot as shown in plot2. Does anyone have an efficient way to do it?
Here is an idea drawing a Gaussian curve through each of the points and then take the maximum of these curves. You might want to experiment with the curve widths.
import matplotlib.pyplot as plt
import numpy as np
low_lim = 30
fc = np.random.rand(120) * np.random.rand(120) * 120
fc = fc[fc > low_lim]
lc = np.random.uniform(50, 250, len(fc))
x = np.linspace(0, 300, 5000)
sigma = 15
ys = np.exp(- np.power((x.reshape(-1, 1) - lc) / sigma, 2) / 2) * fc
ymax = ys.max(axis=1)
fig, (ax1, ax2) = plt.subplots(ncols=2, figsize=(15, 4))
for ax in (ax1, ax2):
if ax == ax1:
ax.plot(x, ymax, color='black', ls=':', lw=3)
for l, f, y in zip(lc, fc, ys.T):
ax.plot(x, y)
ax.fill_between(x, 0, y, color='r', alpha=0.05)
else:
ax.plot(x, ymax, color='black', lw=2)
ax.fill_between(x, 0, ymax, color='r', alpha=0.2)
ax.scatter(lc, fc, color='darkorange')
ax.axhline(low_lim, ls='--', color='skyblue')
ax.set_ylim(ymin=0)
ax.margins(x=0)
plt.tight_layout()
plt.show()
Here is an attempt to smooth out the sharp corners, which might or might not work with your data. The effect is only very local; trying to smooth out more resulted in also losing the general shape.
from scipy.special import softmax
ys = np.exp(- np.power((x.reshape(-1, 1) - lc) / sigma, 2) / 2) * fc
softmax_weights = softmax(np.power(ys, 0.8), axis=1)
ymax = np.sum(ys * softmax_weights, axis=1)
I have the following, self-explanatory situation; please see the figure and working example pasted below.
I wonder how to center text in the middle of the dimension line.
import numpy as np
import matplotlib.pyplot as plt
# Dimension line
def annotation_line(ax, xmin, xmax, y, text, ytext=0, linecolor='black', linewidth=1, fontsize=12):
ax.annotate('', xy=(xmin, y), xytext=(xmax, y), xycoords='data', textcoords='data', arrowprops={'arrowstyle': '|-|', 'color':linecolor, 'linewidth':linewidth})
ax.annotate('', xy=(xmin, y), xytext=(xmax, y), xycoords='data', textcoords='data', arrowprops={'arrowstyle': '<->', 'color':linecolor, 'linewidth':linewidth})
xcenter = xmin + (xmax - xmin) / 2
if ytext==0:
ytext = y + ( ax.get_ylim()[1] - ax.get_ylim()[0] ) / 20
ax.annotate(text, xy=(xcenter, ytext), ha='center', va='bottom', fontsize=fontsize)
# Toy data
N = 8
y = np.zeros(N)
x1 = np.linspace(1, 1000, N, endpoint=True)
fig, ax = plt.subplots(figsize=(10, 6))
ax.plot(x1, y, 'o')
annotation_line(ax=ax, text='TEXT 1', xmin=1, xmax=100, y=0.01, ytext=0, linewidth=1, linecolor='gray', fontsize=12)
ax.set_xscale('log')
The simple solution is to do as #JohanC suggests and calculate the midpoint in log coordinates.
An other solution is to use the coordinates of the arrow to find it's midpoint. There are drawbacks to that method however. First, you need to explicitly draw the figure at an intermediate step, since the coordinates will only be valid at the time of drawing, and second, you need to set the log-scale before drawing the annotation. On the other hand, the code works regardless of the scaling of the axes
import numpy as np
import matplotlib.pyplot as plt
# Dimension line
def annotation_line(ax, xmin, xmax, y, text, ytext=0, linecolor='black', linewidth=1, fontsize=12):
an = ax.annotate('', xy=(xmin, y), xytext=(xmax, y), xycoords='data', textcoords='data', arrowprops={'arrowstyle': '|-|', 'color':linecolor, 'linewidth':linewidth})
ax.annotate('', xy=(xmin, y), xytext=(xmax, y), xycoords='data', textcoords='data', arrowprops={'arrowstyle': '<->', 'color':linecolor, 'linewidth':linewidth})
ax.figure.canvas.draw() # draw to get actual coordinates
p = an.arrow_patch.get_path().transformed(ax.transAxes.inverted())
xmin, xmax = np.min(p.vertices[:,0]),np.max(p.vertices[:,0])
xcenter = xmin+(xmax-xmin)/2
if ytext==0:
ytext = y + ( ax.get_ylim()[1] - ax.get_ylim()[0] ) / 20
ax.annotate(text, xy=(xcenter, ytext), xycoords=('axes fraction','data'), ha='center', va='bottom', fontsize=fontsize)
return an
# Toy data
N = 8
y = np.zeros(N)
x1 = np.linspace(1, 1000, N, endpoint=True)
fig, ax = plt.subplots(figsize=(10, 6))
ax.plot(x1, y, 'o')
ax.set_xscale('log') # must do before the call to annotation_line
an = annotation_line(ax=ax, text='TEXT 1', xmin=1, xmax=100, y=0.01, ytext=0, linewidth=1, linecolor='gray', fontsize=12)