Develop Reference

How can i Plot arrows in a existing mplsoccer pitch?

I tried to do the tutorial of McKay Johns on YT (reference to the Jupyter Notebook to see the data (https://github.com/mckayjohns/passmap/blob/main/Pass%20map%20tutorial.ipynb).
I understood everything but I wanted to do a little change. I wanted to change plt.plot(...) with:
plt.arrow(df['x'][x],df['y'][x], df['endX'][x] - df['x'][x], df['endY'][x]-df['y'][x],
shape='full', color='green')
But the problem is, I still can't see the arrows. I tried multiple changes but I've failed. So I'd like to ask you in the group.
Below you can see the code.
## Read in the data
df = pd.read_csv('...\Codes\Plotting_Passes\messibetis.csv')
#convert the data to match the mplsoccer statsbomb pitch
#to see how to create the pitch, watch the video here: https://www.youtube.com/watch?v=55k1mCRyd2k
df['x'] = df['x']*1.2
df['y'] = df['y']*.8
df['endX'] = df['endX']*1.2
df['endY'] = df['endY']*.8
# Set Base
fig ,ax = plt.subplots(figsize=(13.5,8))
# Change background color of base
fig.set_facecolor('#22312b')
# Change color of base inside
ax.patch.set_facecolor('#22312b')
#this is how we create the pitch
pitch = Pitch(pitch_type='statsbomb',
pitch_color='#22312b', line_color='#c7d5cc')
# Set the axes to our Base
pitch.draw(ax=ax)
# X-Achsen => 0 to 120
# Y-Achsen => 80 to 0
# Lösung: Y-Achse invertieren:
plt.gca().invert_yaxis()
#use a for loop to plot each pass
for x in range(len(df['x'])):
if df['outcome'][x] == 'Successful':
#plt.plot((df['x'][x],df['endX'][x]),(df['y'][x],df['endY'][x]),color='green')
plt.scatter(df['x'][x],df['y'][x],color='green')
**plt.arrow(df['x'][x],df['y'][x], df['endX'][x] - df['x'][x], df['endY'][x]-df['y'][x],
shape='full', color='green')** # Here is the problem!
if df['outcome'][x] == 'Unsuccessful':
plt.plot((df['x'][x],df['endX'][x]),(df['y'][x],df['endY'][x]),color='red')
plt.scatter(df['x'][x],df['y'][x],color='red')
plt.title('Messi Pass Map vs Real Betis',color='white',size=20)
It always shows:

The problem is that plt.arrow has default values for head_width and head_length, which are too small for your figure. I.e. it is drawing arrows, the arrow heads are just way too tiny to see them (even if you zoom out). E.g. try something as follows:
import pandas as pd
import matplotlib.pyplot as plt
from mplsoccer.pitch import Pitch
df = pd.read_csv('https://raw.githubusercontent.com/mckayjohns/passmap/main/messibetis.csv')
...
# create a dict for the colors to avoid repetitive code
colors = {'Successful':'green', 'Unsuccessful':'red'}
for x in range(len(df['x'])):
plt.scatter(df['x'][x],df['y'][x],color=colors[df.outcome[x]], marker=".")
plt.arrow(df['x'][x],df['y'][x], df['endX'][x] - df['x'][x],
df['endY'][x]-df['y'][x], color=colors[df.outcome[x]],
head_width=1, head_length=1, length_includes_head=True)
# setting `length_includes_head` to `True` ensures that the arrow head is
# *part* of the line, not added on top
plt.title('Messi Pass Map vs Real Betis',color='white',size=20)
Result:
Note that you can also use plt.annotate for this, passing specific props to the parameter arrowprops. E.g.:
import pandas as pd
import matplotlib.pyplot as plt
from mplsoccer.pitch import Pitch
df = pd.read_csv('https://raw.githubusercontent.com/mckayjohns/passmap/main/messibetis.csv')
...
# create a dict for the colors to avoid repetitive code
colors = {'Successful':'green', 'Unsuccessful':'red'}
for x in range(len(df['x'])):
plt.scatter(df['x'][x],df['y'][x],color=colors[df.outcome[x]], marker=".")
props= {'arrowstyle': '-|>,head_width=0.25,head_length=0.5',
'color': colors[df.outcome[x]]}
plt.annotate("", xy=(df['endX'][x],df['endY'][x]),
xytext=(df['x'][x],df['y'][x]), arrowprops=props)
plt.title('Messi Pass Map vs Real Betis',color='white',size=20)
Result (a bit sharper, if you ask me, but maybe some tweaking with params in plt.arrow can also achieve that):

How do I create a strip plot similar to this using vega-lite?

I'm interested in being able to recreate this multidimensional strip plot below, generated by the Missing Numbers python library, using vega-lite, and I'm looking for a few pointers on how I might do this. The code to generate the image below looks a bit like this snippet:
>>> from quilt.data.ResidentMario import missingno_data
>>> collisions = missingno_data.nyc_collision_factors()
>>> collisions = collisions.replace("nan", np.nan)
>>> import missingno as msno
>>> %matplotlib inline
>>> msno.matrix(collisions.sample(250))
For each column, there is a mark shown for a specific combination of the index, and where the data is null, or not null.
When I look through a gallery of charts created by Altair, I see this horizontal strip plot, which seems to be presenting a similar kind of information, but I'm not sure how to express the same idea.
The viz below is showing a mark when there is data that matches a given combination of horse power and cylinder size - the horsepower and cylinder are encoded into the x and y channels.
I'm not show how I'd express the same for the cool nullity matrix thing, and I think I need some pointers here.
I get that I can reset and index to come up with a y index, but it's not clear to me how to index of the sample is encoded in the Y channel, I'm not sure how I'd populate the x-axis with a column listing the null/not null results. Is this a thing I'd need to do before it gets to vega-lite, or does vega support it?

Yes, you can do this after reshaping your data with a Fold Transform. It looks something like this using Altair:
import numpy as np
import quilt
quilt.install("ResidentMario/missingno_data")
from quilt.data.ResidentMario import missingno_data
collisions = missingno_data.nyc_collision_factors()
collisions = collisions.replace("nan", np.nan)
collisions = collisions.set_index("Unnamed: 0")
import altair as alt
alt.Chart(collisions.sample(250)).transform_window(
index='row_number()'
).transform_fold(
collisions.columns.to_list()
).transform_calculate(
defined="isValid(datum.value)"
).mark_rect().encode(
x=alt.X('key:N',
title=None,
sort=collisions.columns.to_list(),
axis=alt.Axis(orient='top', labelAngle=-45)
),
y=alt.Y('index:O', title=None),
color=alt.Color('defined:N',
legend=None,
scale=alt.Scale(domain=["true", "false"], range=["black", "white"])
)
).properties(
width=800, height=400
)

Using python and matplotlib, fill between two lines not giving expected output

I am trying to plot a linear line with associated error.
I calculated values for slope (a) and intercepts (b). In addition, I calculated the error associated with these values. So I drew the line given by the typical formula below.
y=ax+b
However, in addition to the line, I also want to draw the associated error. I came up with the idea to draw the lines associated with these formulas and color the space between the lines gray.
y=(a+a_sd)x+(b+b_sd)
y=(a-a_sd)x+(b-b_sd)
Uisng the following piece of code, I am able to color part of the surface between the lines, but not the whole span (see included output).
I think this may be due to the fact that "distance" is not sorted, and fill_between is using distance[0] and distance[-1] as begin and end for the span, respectively.
As always, any help would be highly appreciated!
import matplotlib.pyplot as plt
distance=[0.35645334340084989, 0.55406894241607718, 0.10201413273193734, 0.13401365724625941, 0.71918808865838735, 0.14151335417722818]
time=[2.4004984846346171, 2.4909766335028447, 1.9852064018125195, 1.9083156734132103, 2.6380396934372863, 1.9114505780323543]
time_SD=[0.062393810960652669, 0.056945715242838917, 0.073960838867327183, 0.084111239062664475, 0.026912957190265499, 0.08595664694840538]
distance_SD=[0.035160608598240162, 0.032976715460514235, 0.02782911002465227, 0.035465701695038584, 0.043009444687382707, 0.038387585107200854]
a=1.17887019041
b=1.83339229489
a_sd=0.159771527859
b_sd=0.0762509747218
plt.errorbar(distance,time,yerr=time_SD, xerr=distance_SD, linestyle="None")
abline_values = [(a)*i + (b) for i in distance]
abline_values_plus = [(a+a_sd)*i + (b+b_sd) for i in distance]
abline_values_minus = [(a-a_sd)*i + (b-b_sd) for i in distance]
plt.plot(distance, abline_values,"r")
plt.fill_between(distance,abline_values_minus,abline_values_plus,facecolor='lightgrey', interpolate=True, edgecolors="None")
leg = plt.legend(loc="lower right", frameon=False, handlelength=0, handletextpad=0)
for item in leg.legendHandles:
item.set_visible(False)
plt.show()

In order to use pyplot.fill_between() the list to plot the horizontal coordinate should be sorted. Using an unsorted list of x values is possible, but can lead to undesired results.
Sorting a list can be done using sorted(list).
import matplotlib.pyplot as plt
distance=[0.35645334340084989, 0.55406894241607718, 0.10201413273193734, 0.13401365724625941, 0.71918808865838735, 0.14151335417722818]
time=[2.4004984846346171, 2.4909766335028447, 1.9852064018125195, 1.9083156734132103, 2.6380396934372863, 1.9114505780323543]
time_SD=[0.062393810960652669, 0.056945715242838917, 0.073960838867327183, 0.084111239062664475, 0.026912957190265499, 0.08595664694840538]
distance_SD=[0.035160608598240162, 0.032976715460514235, 0.02782911002465227, 0.035465701695038584, 0.043009444687382707, 0.038387585107200854]
a=1.17887019041
b=1.83339229489
a_sd=0.159771527859
b_sd=0.0762509747218
distance_sorted = sorted(distance)
plt.errorbar(distance,time,yerr=time_SD, xerr=distance_SD, linestyle="None")
abline_values = [(a)*i + (b) for i in distance_sorted]
abline_values_plus = [(a+a_sd)*i + (b+b_sd) for i in distance_sorted]
abline_values_minus = [(a-a_sd)*i + (b-b_sd) for i in distance_sorted]
plt.plot(distance_sorted, abline_values,"r")
plt.fill_between(distance_sorted,abline_values_minus,abline_values_plus, facecolor='lightgrey', edgecolors="None")
plt.show()
The documentation does not mention the requirement of x values being sorted. The reason is probably that fill_between actually works even with unsorted lists, just not the way one might expect. Maybe the following animation gives a more intuitive understanding on the issue:

You are right fill_between seems to expect the values to be sorted. The documentation is not clear about this behaviour though. The following example however shows the same effect:
import matplotlib.pyplot as plt
from numpy import random, array
#x = random.randn(20) #does not work
x = array(sorted(random.randn(20))) #works
a = 2
d = .5
y_h = x*(a+d)
y_l = x*(a-d)
plt.fill_between(x,y_h, y_l)
plt.show()
As a workaround just sort your values before calculating your errorlines using sorted.

Plot spectroscopic data from pandas dataframe in 3D with different array length

Is it possible to get something like this plot
from a pandas dataframe, in a a similar fashion as I would just simply do to do 2d-plots (df.plot())?
More precisely:
I have data that I read from csv files into pandas DataFrames with following structure:
1st level header A B C D E F
2nd level header 2.0 1.0 0.2 0.4 0.6 0.8
Index
126.4348 -467048 -814795 301388 298430 -187654 -1903170
126.4310 -468329 -810060 304366 305343 -192035 -1881625
126.4272 -469209 -804697 305795 312472 -197013 -1854848
126.4234 -469685 -799604 305647 318936 -200957 -1827665
126.4195 -469795 -795708 304101 323922 -202192 -1805153
126.4157 -469610 -793795 301497 326780 -199323 -1791743
126.4119 -469213 -794362 298257 327092 -191547 -1790418
126.4081 -468687 -797499 294817 324717 -178875 -1802122
126.4043 -468097 -802853 291546 319800 -162225 -1825540
126.4005 -467486 -809663 288700 312745 -143334 -1857270
126.3967 -466863 -816878 286401 304170 -124505 -1892389
126.3929 -466210 -823335 284645 294827 -108228 -1925312
126.3890 -465485 -827966 283331 285520 -96733 -1950795
126.3852 -464637 -829997 282315 277018 -91559 -1964894
126.3814 -463617 -829104 281457 269965 -93242 -1965702
126.3776 -462399 -825487 280670 264824 -101170 -1953728
126.3738 -460982 -819857 279942 261819 -113660 -1931820
126.3700 -459408 -813317 279344 260927 -128242 -1904669
126.3662 -457757 -807177 279009 261885 -142112 -1877955
126.3624 -456143 -802715 279090 264233 -152667 -1857303
126.3585 -454700 -800940 279722 267380 -158023 -1847241
126.3547 -453566 -802397 280969 270692 -157406 -1850358
126.3509 -452862 -807050 282792 273579 -151350 -1866803
126.3471 -452672 -814262 285033 275591 -141627 -1894249
126.3433 -453030 -822898 287426 276486 -130942 -1928303
126.3395 -453910 -831501 289627 276273 -122426 -1963297
126.3357 -455223 -838544 291266 275222 -119021 -1993312
126.3319 -456834 -842695 292004 273824 -122882 -2013246
126.3280 -458571 -843048 291599 272725 -134907 -2019718
126.3242 -460252 -839292 289952 272620 -154497 -2011656
... ... ... ... ... ... ...
What I would like to do with that
I would like to plot each of these columns (they are NMR spectra) against the index.
In a 2D overlay, this is simple usage of the pandas wrapper around matplotlib.
However, I would like to plot each spectrum in its own "line", along a third axis that has the second level headers as
ticks.
I tried to use matplotlib´s 3D plotting functionality, but it seems to only be suitable if you actually have three arrays of equal length,
which in the case of my data does just not make sense, because each spectrum is recorded for one of the values from the second level header.
Am I maybe thinking too complicated when I try to make a 3D plot?
Is the figure I would like my plot to look like maybe not an actual 3D plot but rather some special version of overlaid 2D plots?
How I would prefer to do it
Bonus points for:
Using only python
Using only pandas and matplotlib
Already implemented functionality
If there is no obvious python way to do it, I would as well be happy about libraries of other languages that can do the same, such as
R or Octave. I am just not as familiar with these, so I would probably not be able to adapt more hacky solutions in these languages to suit my requirements.
This question might be very similar, but as I understand it, it does not necessarily extend to software other than python and doesn't have an example of what the result should look like, so I am not sure if answers to that question might actually be helpful for this specific purpose.
What is wrong with matplotlib´s gallery examples
As lanery pointed out, polygon3D from the matplotlib gallery gets close to what I wish for.
However it has some drawbacks some of which are not acceptable for most scientific publications:
With negative values, the whole plot gets shifted to what I would
call "the middle of the screen", which looks kind of ugly, makes
it hard to extract information from the figure and makes it different
from the provided examples
You get that interactive plot window, which requires you to find an
angle from which you can see everything you need to see. That
might be good for some data exploration tasks, but if you use
scripts for your visualization and a minor change to the graphic
would force you to do some manual work again, this decreases the
advantage you expect from scripting
If you have values that differ strongly and are not linear, something
like [0,1,1.7,2.5,6.2], for your third dimension i.e. the second
level header in this case, the 2d plots have very different distances
from another, which is unacceptable, at least for any
non-programming audience reading the publications
It is quite long and technical for a quite common plotting operation
in spectroscopy. The amount of code would be fine if I wanted to
build software that can make 3D plots in some context. For science it
would be preferable to be able to accomplish something like this
with a low amount of code.

I gave you an example of plotting with the data from the continuous X and Y, and just hard-coded z based on your second level header.
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import matplotlib
%matplotlib inline
df = pd.read_csv("C:\Users\User\SkyDrive\Documents\import_data.tcsv.txt",header=None)
fig = plt.figure()
ax = fig.gca(projection='3d')
# Plot a sin curve using the x and y axes.
x = df[0]
ax.plot(x, df[1], zs=2, zdir='z', label='A')
ax.plot(x, df[2], zs=1, zdir='z', label='B')
ax.plot(x, df[3], zs=0.2, zdir='z', label='C')
ax.plot(x, df[4], zs=0.4, zdir='z', label='D')
ax.plot(x, df[5], zs=0.6, zdir='z', label='E')
ax.plot(x, df[6], zs=0.8, zdir='z', label='F')
# Customize the view angle so it's easier to see that the scatter points lie
# on the plane y=0
ax.view_init(elev=-150., azim=40)
plt.show()
Your going to have to play with the options on view_init to rotate around and get the axes where you want. I'm not really clear with what your end goal was, but this is the end plot.

Manually setting xticks with xaxis_date() in Python/matplotlib

I've been looking into how to make plots against time on the x axis and have it pretty much sorted, with one strange quirk that makes me wonder whether I've run into a bug or (admittedly much more likely) am doing something I don't really understand.
Simply put, below is a simplified version of my program. If I put this in a .py file and execute it from an interpreter (ipython) I get a figure with an x axis with the year only, "2012", repeated a number of times, like this.
However, if I comment out the line (40) that sets the xticks manually, namely 'plt.xticks(tk)' and then run that exact command in the interpreter immediately after executing the script, it works great and my figure looks like this.
Similarly it also works if I just move that line to be after the savefig command in the script, that's to say to put it at the very end of the file. Of course in both cases only the figure drawn on screen will have the desired axis, and not the saved file. Why can't I set my x axis earlier?
Grateful for any insights, thanks in advance!
import matplotlib.pyplot as plt
import datetime
# define arrays for x, y and errors
x=[16.7,16.8,17.1,17.4]
y=[15,17,14,16]
e=[0.8,1.2,1.1,0.9]
xtn=[]
# convert x to datetime format
for t in x:
hours=int(t)
mins=int((t-int(t))*60)
secs=int(((t-hours)*60-mins)*60)
dt=datetime.datetime(2012,01,01,hours,mins,secs)
xtn.append(date2num(dt))
# set up plot
fig=plt.figure()
ax=fig.add_subplot(1,1,1)
# plot
ax.errorbar(xtn,y,yerr=e,fmt='+',elinewidth=2,capsize=0,color='k',ecolor='k')
# set x axis range
ax.xaxis_date()
t0=date2num(datetime.datetime(2012,01,01,16,35)) # x axis startpoint
t1=date2num(datetime.datetime(2012,01,01,17,35)) # x axis endpoint
plt.xlim(t0,t1)
# manually set xtick values
tk=[]
tk.append(date2num(datetime.datetime(2012,01,01,16,40)))
tk.append(date2num(datetime.datetime(2012,01,01,16,50)))
tk.append(date2num(datetime.datetime(2012,01,01,17,00)))
tk.append(date2num(datetime.datetime(2012,01,01,17,10)))
tk.append(date2num(datetime.datetime(2012,01,01,17,20)))
tk.append(date2num(datetime.datetime(2012,01,01,17,30)))
plt.xticks(tk)
plt.show()
# save to file
plt.savefig('savefile.png')

I don't think you need that call to xaxis_date(); since you are already providing the x-axis data in a format that matplotlib knows how to deal with. I also think there's something slightly wrong with your secs formula.
We can make use of matplotlib's built-in formatters and locators to:
set the major xticks to a regular interval (minutes, hours, days, etc.)
customize the display using a strftime formatting string
It appears that if a formatter is not specified, the default is to display the year; which is what you were seeing.
Try this out:
import datetime as dt
import matplotlib.pyplot as plt
from matplotlib.dates import DateFormatter, MinuteLocator
x = [16.7,16.8,17.1,17.4]
y = [15,17,14,16]
e = [0.8,1.2,1.1,0.9]
xtn = []
for t in x:
h = int(t)
m = int((t-int(t))*60)
xtn.append(dt.datetime.combine(dt.date(2012,1,1), dt.time(h,m)))
def larger_alim( alim ):
''' simple utility function to expand axis limits a bit '''
amin,amax = alim
arng = amax-amin
nmin = amin - 0.1 * arng
nmax = amax + 0.1 * arng
return nmin,nmax
plt.errorbar(xtn,y,yerr=e,fmt='+',elinewidth=2,capsize=0,color='k',ecolor='k')
plt.gca().xaxis.set_major_locator( MinuteLocator(byminute=range(0,60,10)) )
plt.gca().xaxis.set_major_formatter( DateFormatter('%H:%M:%S') )
plt.gca().set_xlim( larger_alim( plt.gca().get_xlim() ) )
plt.show()
Result:
FWIW the utility function larger_alim was originally written for this other question: Is there a way to tell matplotlib to loosen the zoom on the plotted data?