Smooth plots, single color scatterplots

Question

I am having difficulty trying to make a smooth graph. Also, how do I make a scatter plot one color? It seems to automatically make it a range of colors.

I am trying to graph

$$ y = 23.0 + \frac{32.3 - 23.9}{\left[ 1 + \left( \num{3.85e-4} \right) e^{-0.765t} \right]^{1 / \num{3.65e-5}$$

\documentclass{article}

\usepackage{siunitx}
\usepackage{pgfplots} \pgfplotsset{width=10cm,compat=1.16}

\begin{filecontents*}{plots help.csv}
time10,5mnaoh-ch3cooh
0,24
0,24.2
0,23.8
0,24.2
0.5,24
0.5,24.2
0.5,23.8
0.5,24.2
1,24
1,24.2
1,23.8
1,24.2
1.5,24
1.5,24.2
1.5,23.8
1.5,24.2
2,24.1
2,24.8
2,24.6
2,24.6
2.5,24.6
2.5,26.2
2.5,26.3
2.5,25.5
3,25.7
3,27.4
3,27.9
3,26.8
3.5,27.2
3.5,28.2
3.5,29.2
3.5,27.9
4,28.7
4,29
4,30.1
4,28.8
4.5,29.8
4.5,29.7
4.5,30.7
4.5,29.5
5,30.6
5,30.3
5,31.1
5,30
5.5,31.2
5.5,30.7
5.5,31.4
5.5,30.6
6,31.5
6,31
6,31.6
6,31
6.5,31.8
6.5,31.3
6.5,31.8
6.5,31.3
7,31.9
7,31.6
7,31.9
7,31.5
7.5,32
7.5,31.8
7.5,32
7.5,31.6
8,32.1
8,32
8,32
8,31.8
8.5,32.2
8.5,32.1
8.5,32.1
8.5,31.9
9,32.2
9,32.2
9,32.1
9,32
9.5,32.2
9.5,32.3
9.5,32.1
9.5,32.1
10,32.3
10,32.3
10,32.1
10,32.2
10.5,32.3
10.5,32.4
10.5,32.1
10.5,32.2
11,32.3
11,32.4
11,32.2
11,32.3
11.5,32.3
11.5,32.5
11.5,32.2
11.5,32.3
12,32.5
12,32.1
12,32.3
12.5,32.5
12.5,32.1
12.5,32.3
13,32.6
13,32.2
13,32.3
13.5,32.6
13.5,32.2
13.5,32.3
14,32.6
14,32.2
14,32.3
14.5,32.6
14.5,32.1
14.5,32.3
15,32.2
15,32.3
15.5,32.2
15.5,32.3
16,32.2
16,32.4
16.5,32.2
16.5,32.4
17,32.4
17.5,32.4
\end{filecontents*}

\begin{document}

\begin{figure}[htbp!]
  \centering
  \begin{tikzpicture}
    \begin{axis}[
      legend pos=south east,
      title = {},
      xlabel = {time (\(s\))},
      ylabel = {temperature (\(\pm \ \SI{0.3}{\celsius}\))},
      xmin = 0, xmax = 20,
      ymin = 20, ymax = 35,
      xtick = {0, 5, 10, 15, 20},
      ytick = {20, 25, 30, 35},
    ]

      \addplot[only marks, scatter, color=black] table [x=time10, y=5mnaoh-ch3cooh, col sep=comma]{plots help.csv};
      \addlegendentry{data points}

      \addplot[blue, no marks, domain=0:20, samples=300, very thick]{23.9 + (32.3 - 23.9)/((1 + 3.85e-4*exp(-0.765*x))^(1/2.65e-5))};
      \addlegendentry{fitted function}

    \end{axis}
  \end{tikzpicture}
\end{figure}

\end{document}

Thank you.

You can color the marks universally by dropping scatter, i.e. \addplot[only marks] table .... I am wondering who provided you with that fit. The exponent seems enormous. Can't you find a fit which does not have these huge exponent? — , Dec 30 '18 at 23:27
@marmot thank you, the colors work. I wrote a brief python code and those values are what it returned. (scipy.optimize.curve_fit) — Ilyankor, Dec 30 '18 at 23:31
@marmot maybe, but isn't tanh symmetrical over its midpoint? From the data (I have more data sets) it looks like its asymmetrical, I just thought the general logistic function was better. The graph comes out nicely on Desmos and python. Should I just import pictures then? — Ilyankor, Dec 30 '18 at 23:35
@marmot thanks for showing me that, but there isn't a way to graph the original function smoothly? — Ilyankor, Dec 30 '18 at 23:54
I added an attempt of an answer. Still think another fit function might be advantageous, though. But I do like the general aspect of the question, which is why I upvoted it some time ago already. — , Dec 31 '18 at 03:51

Fran · Answer 1 · 2019-01-01T08:04:05.760

One way for knitr users, with a smooth logistic regression of four parameters (4PL).

The less important here is not the color or the smoothness of the curve (no problem with that,however) but the relative facility to obtain a fit to this model (or many others) and plot it with the drc package. Briefly, once you have the data in a "x" and "y" object, to make the 4PL model is simple:

model <- drm(y~x, fct=LL.4())

and plot the model

plot(model)

And that's it. By default print the fitted curve and averages of the observations. If you want to see individual values, or a more fancy plot, we must mess it up a bit more. As we are in the time of gifts, here is a complete example, with individual observations, and fit curve with confidence limits at 99.9%, legends and pointing the four parameters. Somewhat excessive for a MWE, but worth to figure the versatility of these almost precooked plots:

\documentclass[10pt]{article}
\usepackage[sc]{mathpazo} % CM not good for screen shots !
%  Omiting filecontents stuff...  Assuming that "help.csv" already exist.  
% No more boring preamble. Let's rock and roll! 

\begin{document}
<<themodel,warning=F,message=F,echo=F>>=
if(!require(drc)) install.packages("drc")
df <- read.csv(file="help.csv",sep=",", header=T) # The external data
names(df) <-c("x","y") # Do not like long names in my variables
model <- drm(y~x, fct=LL.4(),data=df,separate=T) # The Model (good Kraftwerk song)
b <- signif(summary(model)$coefficients[1],3) # The four parameters of the Apocalipsis
c <- signif(summary(model)$coefficients[2],4)
d <- signif(summary(model)$coefficients[3],4)
e <- signif(summary(model)$coefficients[4],3)
@

The \texttt{LL.4} function of R package \texttt{drc} fit the data according to this four parameter  logistic formula:

\[f(x)=c+\frac{d-c}{1+\exp(b(\log(x)-\log(e)))}\]

Result in the fitted data is: 

\[f(x)=\Sexpr{c}+\frac{\Sexpr{d}-\Sexpr{c}}{1+\exp(\Sexpr{b}(\log(x)-\log(\Sexpr{e})))}\]

<<the4PLplot,warning=F,message=F,echo=F,fig.cap="4PL Regression with 99.9 \\% confidence limits.",dev='tikz',fig.width=5,fig.height=5>>=
plot(model,log="",type="obs",pch=16, col="darkgray", xlab="Time (s)", 
ylab=" Temperature \\(\\pm\\) 0.3 \\(^{\\circ}\\)C ") # The plot !
plot(model,log="",type="confidence", col="blue",lwd=3, 
     confidence.level=.999,add=T) # Again!
# Now just more and more ornaments:
legend("bottomright", inset=c(.05,.05), c("Observed","Fitted"),col=c("darkgray","blue"),
pch=c(16,NA),lwd=c(NA,3))
pree <- predict(model, data.frame(e=e))
arrows(5,c,2,c, length=0.1, col =2, code=2)
text(5.5,c,"c",col=2)
arrows(5,d,8,d, length=0.1, col =2, code=2)
text(4.5,d,"d",col=2)
arrows(e,25,e,pree, length=0.1, lty=1, col ="chocolate4", code=0)
arrows(e,pree,-0.5, pree, length=0.1, lty=1, code=2, col="chocolate4")
text(e,24.5,"e",col="chocolate4")
arrows(e-2,predict(model, data.frame(e=e-1)),
       e,predict(model, data.frame(e=e+1)), 
length=0.1, lty=1, lwd=1, code=3, col="magenta")
text(e-2,pree-1, "b (slope)", srt=75, col="magenta") 
@

\end{document}

score 1 · Answer 2 · 2018-12-31T03:50:01.667

I take this as a question whether one can smoothen out a given function. And the answer is, of course, yes. Since the procedure involves a bit of math and formulae, I typed it up with Word, oh, sorry, LaTeX of course. ;-)

\documentclass[fleqn]{article}

\usepackage{siunitx}
\usepackage{amsmath}
\usepackage{pgfplots} 
\pgfplotsset{width=10cm,compat=1.16}

\usepackage{filecontents}
\begin{filecontents*}{plots-help.csv}
time10,5mnaoh-ch3cooh
0,24
0,24.2
0,23.8
0,24.2
0.5,24
0.5,24.2
0.5,23.8
0.5,24.2
1,24
1,24.2
1,23.8
1,24.2
1.5,24
1.5,24.2
1.5,23.8
1.5,24.2
2,24.1
2,24.8
2,24.6
2,24.6
2.5,24.6
2.5,26.2
2.5,26.3
2.5,25.5
3,25.7
3,27.4
3,27.9
3,26.8
3.5,27.2
3.5,28.2
3.5,29.2
3.5,27.9
4,28.7
4,29
4,30.1
4,28.8
4.5,29.8
4.5,29.7
4.5,30.7
4.5,29.5
5,30.6
5,30.3
5,31.1
5,30
5.5,31.2
5.5,30.7
5.5,31.4
5.5,30.6
6,31.5
6,31
6,31.6
6,31
6.5,31.8
6.5,31.3
6.5,31.8
6.5,31.3
7,31.9
7,31.6
7,31.9
7,31.5
7.5,32
7.5,31.8
7.5,32
7.5,31.6
8,32.1
8,32
8,32
8,31.8
8.5,32.2
8.5,32.1
8.5,32.1
8.5,31.9
9,32.2
9,32.2
9,32.1
9,32
9.5,32.2
9.5,32.3
9.5,32.1
9.5,32.1
10,32.3
10,32.3
10,32.1
10,32.2
10.5,32.3
10.5,32.4
10.5,32.1
10.5,32.2
11,32.3
11,32.4
11,32.2
11,32.3
11.5,32.3
11.5,32.5
11.5,32.2
11.5,32.3
12,32.5
12,32.1
12,32.3
12.5,32.5
12.5,32.1
12.5,32.3
13,32.6
13,32.2
13,32.3
13.5,32.6
13.5,32.2
13.5,32.3
14,32.6
14,32.2
14,32.3
14.5,32.6
14.5,32.1
14.5,32.3
15,32.2
15,32.3
15.5,32.2
15.5,32.3
16,32.2
16,32.4
16.5,32.2
16.5,32.4
17,32.4
17.5,32.4
\end{filecontents*}

\begin{document}
How can one smooth out a function? In mathematics one uses so--called
convolutions for that,
\begin{align}
 f_\mathrm{smooth}(x) &~=~ (f*\delta_\varepsilon)(x)
 ~=~\int\limits_{-\infty}^\infty f(x-y)\,\delta_\varepsilon(y)\,\mathrm{d}y\;,
\end{align}
where $\delta_\varepsilon$ is some smooth bump at the origin. For examle,
\begin{align}
 \delta_\varepsilon(x)&~=~\mathcal{N}_\varepsilon\,\exp\left(-x^2/\varepsilon\right)\;,
\end{align}
where $\varepsilon>0$ and $\mathcal{N}_\varepsilon$ is such that
\begin{align}
 \int\limits_{-\infty}^\infty\delta_\varepsilon(x)\,\mathrm{d}x~=~1\;.
\end{align}
Of course, we cannot implement this in \texttt{pgfplots}, but we can use a
discretized version thereof, e.g.
\begin{align}
 f_\mathrm{a~bit~smooth}(x)&~=~
 \frac{1}{10}\bigl(4f(x)+2f(x+\Delta x)+2f(x-\Delta x)\notag\\
 &\hphantom{~=~ \frac{1}{10}\bigl(}+f(x+2\Delta x)+f(x-2\Delta x)\bigr)\;.
\end{align}

\begin{figure}[htbp!]
  \centering
  \begin{tikzpicture}[declare function={a=28;b=4.5;c=1/2;xnod=4;dx=0.001;
  myfit(\x)=a+b*tanh(c*(\x-xnod));
  smoothfit(\x)=0.1*(4*myfit(\x)+2*myfit(\x+dx)+2*myfit(\x-dx)+myfit(\x+2*dx)+myfit(\x-2*dx));
  }]
    \begin{axis}[
      legend pos=south east,
      title = {},
      xlabel = {time (\(s\))},
      ylabel = {temperature (\(\pm \ \SI{0.3}{\celsius}\))},
      xmin = 0, xmax = 20,
      ymin = 20, ymax = 35,
      xtick = {0, 5, 10, 15, 20},
      ytick = {20, 25, 30, 35},
    ]

      \addplot[only marks] table [x=time10, y=5mnaoh-ch3cooh, col sep=comma]{plots-help.csv};
      \addlegendentry{data points}

      \addplot[blue, no marks, domain=0:20, samples=101,smooth, very
      thick]{smoothfit(\x)};
      \addlegendentry{fitted function}

    \end{axis}
  \end{tikzpicture}
\end{figure}
\clearpage
The bump around 18 can be removed by hand.
\begin{figure}[htbp!]
  \centering
  \begin{tikzpicture}[declare function={a=28;b=4.5;c=1/2;xnod=4;dx=0.001;
  myfit(\x)=a+b*tanh(c*(\x-xnod));
  smoothfit(\x)=0.1*(4*myfit(\x)+2*myfit(\x+dx)+2*myfit(\x-dx)+myfit(\x+2*dx)+myfit(\x-2*dx));
  }]
    \begin{axis}[
      legend pos=south east,
      title = {},
      xlabel = {time (\(s\))},
      ylabel = {temperature (\(\pm \ \SI{0.3}{\celsius}\))},
      xmin = 0, xmax = 20,
      ymin = 20, ymax = 35,
      xtick = {0, 5, 10, 15, 20},
      ytick = {20, 25, 30, 35},
    ]

      \addplot[only marks] table [x=time10, y=5mnaoh-ch3cooh, col sep=comma]{plots-help.csv};
      \addlegendentry{data points}

      \addplot[blue, no marks, samples at={0,0.02,...,15,16,17,18,19,20},smooth, very
      thick]{smoothfit(\x)};
      \addlegendentry{fitted function}

    \end{axis}
  \end{tikzpicture}
\end{figure}

\end{document}

Smooth plots, single color scatterplots

2 Answers2

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