Related
first of all before my sharing my problem I want to share a bit of code that might be helpful for some people outside there. I have been looking quite some time code to plot in 3d antenna measurements but I could not find code that does that. The problem is that antenna measurements have polar coordinates and typical 3d plot functions use cartesian coordinates. So my code below does just that (I am not an advanced programmer so I am sure someone might be able to optimize it for its use). The code can be run directly and I added comments to make it easier readable.
require("rgl")
require("fields")
degreeToRadian<-function(degree){
return (0.01745329252*degree)
}
turnPolarToX<-function(Amplitude,Coordinate){
return (Amplitude*cos(degreeToRadian(Coordinate)))
}
turnPolarToY<-function(Amplitude,Coordinate){
return (Amplitude*sin(degreeToRadian(Coordinate)))
}
# inputs for the code
test<-runif(359,min=-50,max=-20) # the 359 elements correspond to the polar coordinates of 1 to 359
test2<-runif(359,min=-50,max=-20) # the 359 elements correspond to the polar coordinates of 1 to 359
test3<-runif(359,min=-50,max=-20) # the 359 elements correspond to the polar coordinates of 1 to 359
# My three input vectors above are considered to be dBm values, typically unit for antenna or propagation measurements
# I want to plot those on three different 3d planes the XY, the YZ and the ZX. Since the rgl does not support
# polar coordinates I need to cast my polar coordinates to cartesian ones, using the three functions
# defined at the beginning. I also need to change my dBm values to their linear relative ones that are the mW
# Convert my dBm to linear ones
test<-10^(test/10)
test2<-10^(test2/10)
test3<-10^(test3/10)
# Start preparing the data to be plotted in cartesian domain
X1<-turnPolarToX(test,1:359)
Y1<-turnPolarToY(test,1:359)
Z1<-rep(0,359)
X2<-turnPolarToX(test2,1:359)
Y2<-rep(0,359)
Z2<-turnPolarToY(test2,1:359)
X3<-rep(0,359)
Y3<-turnPolarToX(test3,1:359)
Z3<-turnPolarToY(test3,1:359)
# Time for the plotting now
Min<-min(test,test2,test3)
Max<-max(test,test2,test3)
bgplot3d( suppressWarnings (
image.plot( legend.only=TRUE, legend.args=list(text='dBm/100kHz'), zlim=c(Min,Max),col=plotrix::color.scale(seq(Min,Max,length.out=21),c(0,1,1),c(0,1,0),0,xrange=c(Min,Max)))
) # zlim is the colorbar numbers
)
# for below alternatively you can also use the lines3d to get values
points3d(X1,Y1,Z1,col=plotrix::color.scale(test,c(0,1,1),c(0,1,0),0,xrange=c(Min,Max)),add=TRUE)
points3d(X2,Y2,Z2,col=plotrix::color.scale(test2,c(0,1,1),c(0,1,0),0,xrange=c(Min,Max)),add=TRUE)
points3d(X3,Y3,Z3,col=plotrix::color.scale(test3,c(0,1,1),c(0,1,0),0,xrange=c(Min,Max)),add=TRUE)
The problem I have now is that my plotting ideally I would like to be on a log scale that the rgl packet does not support! If I try to use log on my X,Y,Z to compress them I get an error that log is not defined for negative numbers (of course that is correct). How would you think to solve that problem on compressing the axes values when log scale plotting is not supported?
I would like to thank you for your reply
Regards
Alex
It doesn't make sense to apply a log scale to X, Y and Z. Just apply it to your original data, and transform the logged values to polar coordinates.
Since your logged test values are negative, you probably will want to apply an offset; polar coordinates with negative radius values are pretty hard to interpret.
Once you have done that, you can use the axis3d() function to add an axis with arbitrary labels to the plot. For example, if you want the origin to correspond to -50 dBm, you'd skip the transformation to linear coordinates and just add 50. You need to undo this when calculating labels. Here's your example, modified:
require("rgl")
require("fields")
degreeToRadian<-function(degree){
return (0.01745329252*degree)
}
turnPolarToX<-function(Amplitude,Coordinate){
return (Amplitude*cos(degreeToRadian(Coordinate)))
}
turnPolarToY<-function(Amplitude,Coordinate){
return (Amplitude*sin(degreeToRadian(Coordinate)))
}
# inputs for the code
test<-runif(359,min=-50,max=-20) # the 359 elements correspond to the polar coordinates of 1 to 359
test2<-runif(359,min=-50,max=-20) # the 359 elements correspond to the polar coordinates of 1 to 359
test3<-runif(359,min=-50,max=-20) # the 359 elements correspond to the polar coordinates of 1 to 359
# Add an offset of 50 to the values.
test <- test + 50
test2 <- test2 + 50
test3 <- test3 + 50
# Start preparing the data to be plotted in cartesian domain
X1<-turnPolarToX(test,1:359)
Y1<-turnPolarToY(test,1:359)
Z1<-rep(0,359)
X2<-turnPolarToX(test2,1:359)
Y2<-rep(0,359)
Z2<-turnPolarToY(test2,1:359)
X3<-rep(0,359)
Y3<-turnPolarToX(test3,1:359)
Z3<-turnPolarToY(test3,1:359)
# Time for the plotting now
Min<-min(test,test2,test3)
Max<-max(test,test2,test3)
bgplot3d( suppressWarnings (
image.plot( legend.only=TRUE, legend.args=list(text='dBm/100kHz'), zlim=c(Min,Max)-50,col=plotrix::color.scale(seq(Min-50,Max-50,length.out=21),c(0,1,1),c(0,1,0),0,xrange=c(Min,Max)-50))
) # zlim is the colorbar numbers
)
# for below alternatively you can also use the lines3d to get values
points3d(X1,Y1,Z1,col=plotrix::color.scale(test,c(0,1,1),c(0,1,0),0,xrange=c(Min,Max)),add=TRUE)
points3d(X2,Y2,Z2,col=plotrix::color.scale(test2,c(0,1,1),c(0,1,0),0,xrange=c(Min,Max)),add=TRUE)
points3d(X3,Y3,Z3,col=plotrix::color.scale(test3,c(0,1,1),c(0,1,0),0,xrange=c(Min,Max)),add=TRUE)
# Add axes
labels <- pretty(c(-50, -20))
axis3d("x", at = labels + 50, labels = labels, pos = c(NA, 0, 0) )
axis3d("y", at = labels + 50, labels = labels, pos = c(0, NA, 0) )
axis3d("z", at = labels + 50, labels = labels, pos = c(0, 0, NA) )
One my system it produces this display:
You might want to add circles to show how the scale continues around in each plane. This code would do it:
theta <- seq(0, 2*pi, len = 100)
for (i in seq_along(labels)) {
x <- (labels[i] + 50)*cos(theta)
y <- (labels[i] + 50)*sin(theta)
lines3d(x, y, 0)
lines3d(x, 0, y)
lines3d(0, x, y)
}
I find the plot too busy with those added, but you can try it and decide for yourself.
I am trying to plot this formula. As x approaches 0 from the right, y should be approaching infinity, and so my curve should be going upwards close to y-axis. Instead it gets cut off at y=23 or so.
my_formula = function(x){7.9*x^(-0.5)-1.3}
curve(my_formula,col="red",from=0 ,to=13, xlim=c(0,13),ylim=c(0,50),axes=T, xlab=NA, ylab=NA)
I tried to play with from= parameter, and actually got what I needed when I
put from=-4.8 but I have no idea why this works. in fact x doesn't get less than 0, and from/to should represent the range of x values, Do they? If someone could explain it to me, this would be amazing! Thank you!
By default, curve only chooses 101 x-values within the (from, to) range, set by the default value of the n argument. In your case this means there aren't many values that are close enough to 0 to show the full behaviour of the function. Increasing the number of values that are plotted with something like n=500 helps:
curve(my_formula,col="red",from=0 ,to=13,
xlim=c(0,13),ylim=c(0,50),axes=T, xlab=NA, ylab=NA,
n=500)
This is due mainly to the fact that my_formula(0) is Inf:
So plotting from=0, to=13 in curve means your first 2 values are by default (with 101 points as #Marius notes):
# x
seq(0, 13, length.out=101)[1:2]
#[1] 0.00 0.13
# y
my_formula(seq(0, 13, length.out=101)[1:2])
#[1] Inf 20.61066
And R will not plot infinite values to join the lines from the first point to the second one.
If you get as close to 0 on your x axis as is possible on your system, you can make this work a-okay. For instance:
curve(my_formula, col="red", xlim=c(0 + .Machine$double.eps, 13), ylim=c(0,50))
I've been struggling to get a plot that shows my data accurately, and spent a while getting gap.plot up and running. After doing so, I have an issue with labelling the points.
Just plotting my data ends up with this:
Plot of abundance data, basically two different tiers of data at ~38,000, and between 1 - 50
As you can see, that doesn't clearly show either the top or the bottom sections of my plots well enough to distinguish anything.
Using gap plot, I managed to get:
gap.plot of abundance data, 100 - 37000 missed, labels only appearing on the lower tier
The code for my two plots is pretty simple:
plot(counts.abund1,pch=".",main= "Repeat 1")
text(counts.abund1, labels=row.names(counts.abund1), cex= 1.5)
gap.plot(counts.abund1[,1],counts.abund1[,2],gap=c(100,38000),gap.axis="y",xlim=c(0,60),ylim=c(0,39000))
text(counts.abund1, labels=row.names(counts.abund1), cex= 1.5)
But I don't know why/can't figure out why the labels (which are just the letters that the points denote) are not being applied the same in the two plots.
I'm kind of out of my depth trying this bit, very little idea how to plot things like this nicely, never had data like it when learning.
The data this comes from is originally a large (10,000 x 10,000 matrix) that contains a random assortment of letters a to z, then has replacements and "speciation" or "immigration" which results in the first lot of letters at ~38,000, and the second lot normally below 50.
The code I run after getting that matrix to get the rank abundance is:
##Abundance 1
counts1 <- as.data.frame(as.list(table(neutral.v1)))
counts.abund1<-rankabundance(counts1)
With neutral.v1 being the matrix.
The data frame for counts.abund1 looks like (extremely poorly formatted, sorry):
rank abundance proportion plower pupper accumfreq logabun rankfreq
a 1 38795 3.9 NaN NaN 3.9 4.6 1.9
x 2 38759 3.9 NaN NaN 7.8 4.6 3.8
j 3 38649 3.9 NaN NaN 11.6 4.6 5.7
m 4 38639 3.9 NaN NaN 15.5 4.6 7.5
and continues for all the variables. I only use Rank and Abundance right now, with the a,x,j,m just the variable that applies to, and what I want to use as the labels on the plot.
Any advice would be really appreciated. I can't really shorten the code too much or provide the matrix because the type of data is quite specific, as are the quantities in a sense.
As I mentioned, I've been using gap.plot to just create a break in the axis, but if there are better solutions to plotting this type of data I'd be absolutely all ears.
Really sorry that this is a mess of a question, bit frazzled on the whole thing right now.
gap.plot() doesn't draw two plots but one plot by decreasing upper section's value, drawing additional box and rewriting axis tick labels. So, the upper region's y-coordinate is neither equivalent to original value nor axis tick labels. The real y-coordinate in upper region is "original value" - diff(gap).
gap.plot(counts.abund1[,1], counts.abund1[,2], gap=c(100,38000), gap.axis="y",
xlim=c(0,60), ylim=c(0,39000))
text(counts.abund1, labels=row.names(counts.abund1), cex= 1.5)
text(counts.abund1[,1], counts.abund1[,2] - diff(c(100, 38000)), labels=row.names(counts.abund1), cex=1.5)
# the example data I used
set.seed(1)
counts.abund1 <- data.frame(rank = 1:50,
abundance = c(rnorm(25, 38500, 100), rnorm(25, 30, 20)))
I try to plot 3D graph on Maple18. I plot 2 graphs on the same plane and I want it to show all intercepts. I actually want only integral intercepts if it's possible but I don't know the command.
Here is the graph I want it to show the intercepts
plot3d([x^2, 3^6*z-432], x = -50 .. 50, z = 0 .. 20)
If you are interested in just showing the intersection of the two expressions, you might try the plots:-intersectplot command. The following will show the intersection for the two surfaces:
p1 := plots:-intersectplot(y=x^2, y=3^6*z-432, x=-50..50, z=0..20, y=0..14000);
If you want to then superimpose this on your original plot:
p2 := plot3d([x^2, 3^6*z-432], x=-50..50, z=0..20):
plots:-display([p1,p2]);
if I make a graph g:
g <- read.table(text="
A B W
1 55 3
2 55 5
3 99 6 ",header=TRUE)
library(igraph)
g <- graph.data.frame(g)
and matrix of coordinates:
y<-1:5
x<-c(0.1,0.1,0.2,0.2,0.8)
l<-data.frame(x,y)
l<-as.matrix(l)
I can plot the graph with node positions according to custom coordinates and plot axes.
plot(g,layout=l,rescale=F,axes=TRUE,ylim=c(0,6),xlim=c(0,1))
But the xaxis limits do not function properly and I think are altered by yaxis limits. How can I control the xaxis they way i want for instance keeping it between 0 and 1.
i.e. plot(x,y,xlim=c(0,1),ylim=c(0,6))
Is this a bug? If it is and this cannot be solved is there another package that would have the same functionality?
The short answer is, you need to set the asp argument of the call to plot to 0 as the default is asp = 1 which produces the behavior you see (i.e., it's not a bug, it's a feature). The long answer with explanation follows.
As you noticed correctly, xaxis varies according to yaxis. Specifically, the x-axis has approxamitely the same distance between high and low numbers as yaxis:
If yaxis = c(0,6), the x-axis goes from -3 to 4. 6 - 0 = 6 and 4 - (-3) = 7
If yaxis = c(0,3), the x-axis goes from -1 to 2. 3 - 0 = 2 - (-1) = 3
Igraph seems to keep a constant ratio between the axes.
If you call ?plot.igraph (the plotting function called with an igraph object, can also be found via help(package = "igraph")), you find under See Also:
igraph.plotting for the detailed description of the plotting
parameters
And if you click on this link (or call ?igraph.plotting)and go through the parameters you will find:
asp A numeric constant, it gives the asp parameter for plot, the aspect ratio. Supply 0 here if you don't want to give an aspect ratio.
It is ignored by tkplot and rglplot.
Defaults to 1.
Hence the aspect parameter asp defaults to 1 in igraph. If you want another ratio, set it to 0:
plot(g,layout=l,rescale=F,axes=TRUE,ylim=c(0,6),xlim=c(0,1), asp = 0)
This answers your question. However, note that the points are now rather big. You will probably want to play around with the following parameters (found on ?igraph.plotting but note that many of the parameters need to be prefixed by vertex. as done by me):
vertex.size Default is 15, 5 seems better
vertex.label.cex Default is 1, 0.8 seems better.
The following produces a nicer plot:
plot(g,layout=l,rescale=F,axes=TRUE,ylim=c(0,6),xlim=c(0,1), asp = 0, vertex.size = 5, vertex.label.cex = 0.8)