How to join function to grid scale?

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Yes, latex+sagetex+tikz is really powerful, but the answer to your question is: it can't be used as you're attempting with the Altermundus packages. The basic problem, I think, is that package designers don't design their package to plot using Sage so attempts to force it as the engine can result in problems like you encountered. I eventually learned of that problem (just like you) as I experimented with using Sage as the plotting engine. My experiments in plotting with sagetex show it works best with pgfplots. Uploading pictures to this site seems to be prevented since the site was hacked so I've put together a post on using sagetex to plot with scaled axes (using pgfplots and the picture from the Altermundus manual). It's here. And this is the template.

\documentclass{standalone}
\usepackage{sagetex}
\usepackage[usenames,dvipsnames]{xcolor}
\usepackage{pgfplots}
\pagestyle{empty}
\begin{document}
\begin{sagesilent}
t = var('t')
LowerX = -6
UpperX = 3
LowerY = -2
UpperY = 6
step = .01
Scale = 1.2
xscale=1
yscale=.5
x_coords = [t for t in srange(LowerX,UpperX,step)]
y_coords = [((-t^2+t+2)*exp(t)).n(digits=6) for t in srange(LowerX,UpperX,step)]

output = r""
output += r"\begin{tikzpicture}[scale=%f]"%(Scale)
output += r"\begin{axis}["
output += r"    grid = both,"
output += r"minor tick num=4,"
output += r"every major grid/.style={Red!30, opacity=1.0},"
output += r"every minor grid/.style={ForestGreen!30, opacity=1.0},"
output += r"height= %f\textwidth,"%(yscale)
output += r"width = %f\textwidth,"%(xscale)
output += r"thick,"
output += r"black,"
output += r"scale=%f,"%(Scale)
output += r"axis lines=center,"
output += r"domain=%f:%f"%(LowerX,UpperX)
output += r"samples=500,"
output += r"xlabel={$\omega,c^{-1}$},ylabel={$M_c,HM$},"
output += r"every axis x label/.style={"
output += r"at={(ticklabel* cs:1.03)},anchor=west,},"
output += r"every axis y label/.style={"
output += r"at={(ticklabel* cs:1.05)},anchor=south,},"
output += r"line join=bevel,"
output += r"xmin=%f,xmax=%f,ymin= %f,ymax=%f]"%(LowerX,UpperX,LowerY, UpperY)
output += r"\addplot[NavyBlue,unbounded coords=jump] coordinates {"
for i in range(0,len(x_coords)-1):
    if (y_coords[i])<LowerY or (y_coords[i])>UpperY:
        output += r"(%f , inf) "%(x_coords[i])
    else:
        output += r"(%f , %f) "%(x_coords[i],y_coords[i])
    output += r"};"

u = var('u')
f = (-u^2+u+2)*exp(u)
m(u) = diff(f,u,1)
tan_line(u)=m(0)*u+2
x1_coords = [u for u in srange(-2.6,1.8,.01)]
y1_coords = [tan_line(u) for u in srange(-2.6,1.8,.01)]

output += r"\addplot[Peach,unbounded coords=jump] coordinates {"
for i in range(0,len(x1_coords)-1):
    if (y_coords[i])<LowerY or (y1_coords[i])>UpperY:
        output += r"(%f , inf) "%(x1_coords[i])
    else:
        output += r"(%f , %f) "%(x1_coords[i],y1_coords[i])
output += r"};"
output += r"\end{axis}"
output += r"\end{tikzpicture}"
\end{sagesilent}
\sagestr{output}
\end{document}

EDIT: I've added code to address axis labels and position. I noted the same problems ... (more)