Looking for custom zticklabels and fontsize too on the z-axis. Most notably the intuitive approach of using zticks([-(R+r),0,R+r],["-R-r","0","R+r"],fontsize=16) does not work. I am using Julia 4.3.0 because this is an older project which I cannot fully convert to a newer version at this time. The commented lines below include additional commands I tried which were unsuccessful.
My final goal here is to get the -0.8, 0, 0.8 values on the z-axis to instead say "-r", and "0" and "r" respectively.
using PyPlot
colormapp = "nipy_spectral"
R = 1.6;
r = 0.8;
N = 256;
dx = 2*pi/(N-1);
y = zeros(N,1); # y = phi (col) toroidal
x = y.'; # x = theta (row) poloidal
for ix = 2:N; y[ix] = (ix-1)*dx; x[ix] = (ix-1)*dx; end
cosxsqr = cos(x) .+ 0.0*y;
sinxsqr = sin(x) .+ 0.0*y;
sinysqr = 0.0*x .+ sin(y);
cosysqr = 0.0*x .+ cos(y);
Rrcosxsqr = R+r*cosxsqr;
rRrcosx = r*Rrcosxsqr[:];
Xsqr = Rrcosxsqr.*cosysqr;
Ysqr = Rrcosxsqr.*sinysqr;
Zsqr = r*sinxsqr;
figure(98)
clf()
pmeshtor = pcolormesh(x,y,Zsqr+r,cmap=colormapp);
cb = colorbar();
colorvals = Zsqr+r;
colorvals = colorvals/maximum(colorvals[:])
ax = figure(99)
clf()
srf = surf(Xsqr,Ysqr,Zsqr,cstride=10,rstride=10,facecolors=get_cmap(colormapp).o((colorvals)))
cb = colorbar(pmeshtor,ticks=[0,0.8,1.6])
cb[:ax][:set_yticklabels](["-r","0","r"], fontsize=16)
xlabel("x",fontsize=16)
ylabel("y",fontsize=16)
zlabel("z",fontsize=16)
xlim([-(R+r)-0.3,R+r+0.3])
ylim([-(R+r)-0.3,R+r+0.3])
zlim([-(R+r)-0.3,R+r+0.3])
xticks([-(R+r),0,R+r],["-R-r","0","R+r"],fontsize=16)
yticks([-(R+r),0,R+r],["-R-r","0","R+r"],fontsize=16)
zticks([-r,0,r])
#zticklabels([-r,0,r],["-r","0","r"])
#setp(ax[:get_zticklabels](),fontsize=16);
#setp(ax[:set_zticklabels](["-r","0","r"]))#,fontsize=16);
Here is the resulting image.
The commented command
setp(ax[:set_zticklabels](["-r","0","r"]),fontsize=16);
does work, but only if insert missing projection option as follows in Fig 99
figure(99)
ax = subplot(111, projection="3d")
Related
My interactive plot (topoplot) reacts to mouse signals, but how to make it reacting to keyboard signals?
Here is my code:
f = Figure()
xs = 1:1:193 #range(-30, 120, length = size(dat_e, 2))
sg = SliderGrid(f[2, 1],
(label="time", range=xs, format = "{:d} ms", startvalue = 100),
)
time = sg.sliders[1].value
str = lift(t -> "[$t ms]", time)
topo_slice = lift((t, data) -> mean(data[1:30, t, :], dims=2)[:,1], time, dat_e)
topo_axis = Axis(f[1, 1], aspect = DataAspect())
topo = eeg_topoplot!(topo_axis, topo_slice,
raw.ch_names[1:30];
positions=pos, # produced automatically from ch_names
label_text=true) # aspect ratio, correlation of height and width
text!(topo_axis, 1, 1, text = str, align = (:center, :center))
#topo_slice = lift((t, data) -> data[:, :, t], time, topo)
xlims!(-0.2, 1.1)
ylims!(-0.2, 1.2)
hidedecorations!(topo_axis)
hidespines!(topo_axis)
f
There is an official instruction https://docs.juliahub.com/AbstractPlotting/6fydZ/0.12.11/interaction.html, but as usual with Julia documentations, there is no example and I have no idea how implement it in my code.
How my plot looks like:
Expanding on the answer from before:
T = 10
pts = range(-1, 1, length=100)
ts = reshape(1:T, 1, 1, :)
topo = cos.(pts) .+ cos.(ts .* pts')
fig = Figure()
ax = Axis(fig[1, 1])
sg = SliderGrid(fig[2,1],
(label="time", range=1:T))
time = sg.sliders[1].value
str = lift(t -> "[$t ms]", time)
text!(ax, str)
topo_slice = lift((t, data) -> data[:, :, t], time, topo)
# decrement/increment slider with left/right keys
on(events(fig).keyboardbutton) do btn
if btn.action in (Keyboard.press, Keyboard.repeat)
if btn.key == Keyboard.left
set_close_to!(sg.sliders[1], time[] - 1)
elseif btn.key == Keyboard.right
set_close_to!(sg.sliders[1], time[] + 1)
end
end
end
contour!(ax, topo_slice)
hidedecorations!(ax)
hidespines!(ax)
fig
I have a trivial piece of code that calculates some quantity and plots it as contours:
%Calculate Biot number vs. h for a selected material
h = (0:5:1000)';
mat = "Copper";
lambda = 386;
r = (0:0.25:50); %In cm
R = r./100; %In m
%Calculate matrix of Bi values
% R = length(h) x C = length(r)
Bi = (h.*R)/lambda;
%Contour Plot of results
%Set boundaries at Bi = 0, 0.1, 1
conts = [0, 0.1, 1];
ptitle = ["Biot Number for a ", mat, " Sphere"];
%Create a personalized colormap with 30 values.
% 0<Bi<0.1 Green
% 0.1<=Bi<1 Yellow
% Bi >= 1 Red
my_green = [229,255,204]./255;
my_yellow = [255,255,204]./255;
my_pink = [255,229,204]./255;
my_cmap = [repmat(my_green, 10, 1); repmat(my_yellow, 10, 1); repmat(my_pink, 10, 1) ];
clf;
colormap (my_cmap);
contourf(h, r, Bi, conts, 'showtext', 'on');
title(ptitle)
xlabel ("h(W/m^2*K)");
ylabel ("r(cm)");
The result is missing the intermediate color (yellow):
What can be done about this?
You have too few contours, so the wrong color is chosen. If you do contourf(h, r, Bi, 0:0.2:1, 'showtext', 'on'); you get:
Also, I'd suggest to make the "green" and the "yellow" more different, as it might be difficult to differentiate them on some displays.
Here's what I meant by "playing around with L, M, N:
conts = [0, 0.1, 1];
ptitle = ["Biot Number for a ", mat, " Sphere"];
%Create a personalized colormap
my_green = [229,255,204]./255;
my_yellow = [255,255,204]./255;
my_pink = [255,229,204]./255;
my_cmap = [repmat(my_green, 10, 1); repmat(my_yellow, 90, 1); repmat(my_pink, 1, 1) ];
figure(); contourf(h, r, Bi, conts, 'showtext', 'on');
colormap (my_cmap);
caxis([0 1.01])
title(ptitle)
xlabel ("h(W/m^2*K)");
ylabel ("r(cm)");
BTW, I ran this on MATLAB R2018a in case you're wondering why you're not getting the exact same thing.
Adding the code below to define countours and to generate the colormap, the process can be automated.
conts = [0, 0.05, 0.1, 0.3, 0.7, 1];
%Create a personalized colormap with 50 values distributed proportionally to Bi values
step = 50/max(max(Bi));
L = ceil(step*0.1);
M = ceil(step*(1-0.1));
H = ceil(step*(max(max(Bi))-1));
my_green = [229,255,204]./255;
my_yellow = [255,255,204]./255;
my_pink = [255,229,204]./255;
my_cmap = [repmat(my_green, L, 1); repmat(my_yellow, M, 1); repmat(my_pink, H, 1)];
Obtaining:
I'm trying to create a phylogeny where the branch lengths that I've coded are represented by colour rather than length. So I want the branch lengths to be equal.
Here is my code:
plotBranchbyTrait(tree.scaled, tree.scaled$edge.length, mode=c("edges"),palette="rainbow", use.edge.length = FALSE, node.depth = 2)
It's my understanding that use.edge.length = FALSE should make the branch lengths equal, and it does this if I code the tree using plot.phylo(). But the tree still shows up with the branch lengths when I use plotBranchbyTrait(). Anyone know how to get around this?
Unfortunately, optional arguments (...) are not directly passed to plot.phylo in the plotBranchbyTrait function. One non-elegant way to fix that is to modify the body directly in R to add a hard coded use.edge.length = FALSE option.
You can do this by creating a new function and modify it using body(foo)[[line_of_interest]] <- substitute(my_new_line <- that_does_something). The following example should work:
## Back up the function
plotBranchbyTrait_no_edge_length <- phytools::plotBranchbyTrait
## The line to modify:
body(plotBranchbyTrait_no_edge_length)[[34]]
# xx <- plot.phylo(tree, type = type, show.tip.label = show.tip.label,
# show.node.label = show.node.label, edge.color = colors, edge.width = edge.width,
# edge.lty = edge.lty, font = font, cex = cex, adj = adj, srt = srt,
# no.margin = no.margin, root.edge = root.edge, label.offset = label.offset,
# underscore = underscore, x.lim = x.lim, y.lim = y.lim, direction = direction,
# lab4ut = lab4ut, tip.color = tip.color, plot = plot, rotate.tree = rotate.tree,
# open.angle = open.angle, lend = 2, new = FALSE)
## Modify the line 34 by adding `use.edge.length = FALSE`
body(plotBranchbyTrait_no_edge_length)[[34]] <- substitute( xx <- plot.phylo(use.edge.length = FALSE, tree, type = type, show.tip.label = show.tip.label, show.node.label = show.node.label, edge.color = colors, edge.width = edge.width, edge.lty = edge.lty, font = font, cex = cex, adj = adj, srt = srt, no.margin = no.margin, root.edge = root.edge, label.offset = label.offset, underscore = underscore, x.lim = x.lim, y.lim = y.lim, direction = direction, lab4ut = lab4ut, tip.color = tip.color, plot = plot, rotate.tree = rotate.tree, open.angle = open.angle, lend = 2, new = FALSE) )
## Testing whether it worked
library(phytools)
tree <- pbtree(n=50)
x <- fastBM(tree)
## With use.edge.length = TRUE (default)
plotBranchbyTrait(tree, x, mode = "tips", edge.width = 4, prompt = FALSE)
## With use.edge.length = FALSE
plotBranchbyTrait_no_edge_length(tree, x, mode = "tips", edge.width = 4, prompt = FALSE)
You can find more on how to modify functions here.
so I am in dire need of help. I have finally managed to construct my R-INLA model and get it to graph as needed. via the code below:
First I create the stacks (note this is the very end of my INLA process, the mesh etc has already been done)
stk.abdu = inla.stack(data = list(y = 1, e = 0), A = list(abdu.mat, 1),tag = 'abdu', effects = list(list(i = 1:sc.mesh.5$n), data.frame(Intercept = 1,dwater=winter.abdu$dwater,elev=winter.abdu$elev,forest=winter.abdu$forest,developed=winter.abdu$developed,openwater=winter.abdu$OpenWater,barren=winter.abdu$barren,shrubland=winter.abdu$shrubland,herb=winter.abdu$herb,planted=winter.abdu$planted,wetland=winter.abdu$wetland,dist=winter.abdu$dwater)))
stk.quad = inla.stack(data = list(y = 0, e = 0.1), A = list(quad.mat, 1),tag = 'quad', effects = list(list(i = 1:sc.mesh.5$n), data.frame(Intercept = 1,dwater=dummy$dwater,elev=dummy$elev,forest=dummy$forest,developed=dummy$developed,openwater=dummy$openwater,barren=dummy$barren,shrubland=dummy$shrubland,herb=dummy$herb,planted=dummy$planted,wetland=dummy$wetland,dist=dummy$dwater)))
stk.prd<-inla.stack(data = list(y = NA), A = list(Aprd, 1),tag = 'prd', effects = list(list(i = 1:sc.mesh.5$n), data.frame(Intercept = 1,dwater=prddf2$dwater,elev=prddf2$elev,forest=prddf2$forest,developed=prddf2$developed,openwater=prddf2$openwater,barren=prddf2$barren,shrubland=prddf2$shrubland,herb=prddf2$herb,planted=prddf2$planted,wetland=prddf2$wetland,dist=prddf2$dwater)))
stk.all.prd = inla.stack(stk.abdu,stk.quad,stk.prd)
Next I fit my model
ft.inla.prd<-inla(y ~ 0 + Intercept + elev + dwater + forest+ developed + f(inla.group(dist,n=50,method="quantile"),model="rw1",scale.model=TRUE)+f(i,model=sc.spde),family="binomial",data=inla.stack.data(stk.all.prd),control.predictor = list(A = inla.stack.A(stk.all.prd),compute=TRUE),E=inla.stack.data(stk.all.prd)$e,control.compute=list(dic = TRUE),control.fixed=list(expand.factor.strategy="INLA"))
Then I change the predicted values from logit to probabilities
ft.inla.prd$newfield <- exp(ft.inla.prd$summary.random$i$mean)/(1 + exp(ft.inla.prd$summary.random$i$mean))
And finally I use inla.mesh.project and levelplot to create my image
xmean <- inla.mesh.project(projgrid,ft.inla.prd$newfield)
levelplot(xmean, col.regions=topo.colors(99), main='Probability of Presence',xlab='', ylab='', scales=list(draw=FALSE))
So my problem is that I now want to export this data (what is projected as the graph) as a raster so that I can work with it in ArcGIS. However, I have not been able to find a way to do so.
Any input is greatly appreciated
I have been working on a program in Scilab that numerically integrates a function by the trapezoidal rule (without using the built-in function). I have no problem with the integration or plotting the function, but I want to overlay the real function on a plot of the trapezoids, colored in.
For some reason, when I set the bounds a = 0 to b = 3, no problem, I get exactly what I want. However, when I set the bounds above 3, the trapezoids will still plot (by lines), but they won't be colored in. In the code below, the color stops at 3. If I plot 0 to 6, for example, the color stops half-way through. 3 to 6, and there is no color at all.
Here are the relevant sections of code:
deff('[y] = f(x)','y = e^(x^2)'); // Definition of function
a = 0; // Lower bound
b = 4; // Upper bound
n = 20; // Number of intervals
h = ((b - a)/n); // Interval spacing
x = a:h:b; // Array of positions for division
and
for i = 1:n+1
y(i) = f(x(i));
end
and
for i = 1:n // Plot colored trapezoids
x_start = a+(h*(i-1));
x_end = a+(h*(i));
y_start = y(i);
y_end = y(i+1);
xpts = [x_start, x_end, x_end, x_start];
ypts = [y_start, y_end, 0, 0];
xfpoly(xpts,ypts,3);
end
This is the plot output for a = 0, b = 3
What version of Scilab are you using?
I tried your code with Scilab 5.4.1 (64bit) and I got uncolored trapezoids, but with 5.5.2 (64bit) all the shapes are nice green.
So maybe there was some bugfix between these versions.
I also changed your function definition from 'y = e^(x^2)' to 'y = %e^(x^2)' since the Euler number is a predefined variable (at least in 5.5.2).
clc;
clear;
deff('[y] = f(x)','y = %e^(x^2)'); // Definition of function
a = 0; // Lower bound
b = 6; // Upper bound
n = 100; // Number of intervals
h = ((b - a)/n); // Interval spacing
x = a:h:b; // Array of positions for division
for i = 1:n+1
y(i) = f(x(i));
end
scf(0);
clf(0);
plot2d(x,y);
for i = 1:n // Plot colored trapezoids
x_start = a+(h*(i-1));
x_end = a+(h*(i));
y_start = y(i);
y_end = y(i+1);
xpts = [x_start, x_end, x_end, x_start];
ypts = [y_start, y_end, 0, 0];
xfpoly(xpts,ypts,3);
end