Does anyone know how to draw multiple 3d plots in one picture using RGL in R Statistics.
I have three variables and each of those variables belong to two groups. I want each group to have a different color so I can visualize it. In regular R stats, I just use subset and then use par(new=T). I haven't seen anything equivalent for the 3d plot. Does anyone have any suggestion?
Thanks!
try plot3d(x, y, z, add=TRUE)
Admittedly I was a bit surprised when it worked, I thought it would throw an error on the first plot, but i guess it creates an existing plot if none exists and otherwise adds the points to the existing plot
Related
I would like to create a ggplot2 layer that includes multiple geom_bspline(), or something similar, to point to regions on different plots after combining them into a single figure. A feature in the data seen in one plot appears in another plot after a transformation. However, it may not be clear to a non-expert they are due to the same phenomenon. The plots are to be combined into a single figure using ggarrange(), cowplot(), patchwork() or something similar.
I can get by using ggforce::geom_ellipse() on each plot but it's not as clean. Any suggestions?
Of course, after asking the question and staring at the figure in question, it came to me that I simply need to add a geom_bspline() to the combined figure. Tried that earlier but didn't give enough thought to the coordinates on the new layer. The coordinates of the spline are given in the range of 0 to 1 for both the x and y values on this new layer. Simple and obvious.
I have a plotting problem with curves when using mixtools
Using the following R code
require(mixtools)
x <- c(rnorm(10000,8,2),rnorm(10000,18,5))
xMix <- normalmixEM(x, lambda=NULL, mu=NULL, sigma=NULL)
plot(xMix, which = 2, nclass=25)
I get a nice histogram, with the 2 normal curves estimated from the model superimposed.
The problem is with the default colours (i.e. red and green), which I need to change for a publication to be black and grey.
One way I thought to doing this was first to produce the histogram
hist(xMix$x, freq=FALSE, nclass=25)
and then add the lines using the "curve" function.
....... but I lost my way, and couldn't solve it
I would be grateful for any pointers or the actual solution
thanks
PS. Note that there is an alternative work-around to this problem using ggplot:
Any suggestions for how I can plot mixEM type data using ggplot2
but for various reasons I need to keep using the base graphics
You can also edit the colours directly using the col2 argument in the mixtools plotting function
For example
plot(xMix, which = 2, nclass=25, col2=c("dimgrey","black"))
giving the problem a bit more thought, I managed to rephrase the problem and ask the question in a much more direct way
Using user-defined functions within "curve" function in R graphics
this delivered two nice solutions of how to use the "curve" function to draw normal distributions produced by the mixture modelling.
the overall answer therefore is to use the "hist" function to draw a histogram of the raw data, then the "curve" function (incorporating the sdnorm function) to draw each normal distribution. This gives total control of the colours (and potentially any other graphic parameter).
And not to forget - this is where I got the code for the sdnorm function - and other useful insights
Any suggestions for how I can plot mixEM type data using ggplot2
Thanks as always to StackOverflow and the contributors who provide such helpful advice.
I would like to draw $3$ dimensional scatter plots, or more precisely I have a program that gives me the mass distribution in the unit cube with respect to a 3 dimensional equidistant grid. You can interpret this as a continuous relaxation of a $3$ dimensional assignment problem if you want.
Anyway this is just to give you a very brief background since my actual problem is not really concerned with the maths behind the procedure but with the visualization. I have:
$n$ points in the unit cube $[0,1]^3$
each of the $n$ points is assigned a "weight" between $0$ and $\frac1n$ (typically a lot of the weights coincide, if there are too many different values, i use the cut command to reduce the range to, say $60$ different values)
And I'd like to plot the $n$ points in a color which corresponds to their weight.
Now I found the rgl Package in R which allows me to do exactly that and also provides a very nice interactive plot window but it doesn't seem to allow a "col key" parameter, i.e. I cannot add a continuous color legend to my plot.
On the other hand the package plot3D provides a function to do a $3$ dimensional scatterplot and easily allows me to add the col key. However plot3D does not work with interactive plots but merely gives me the option to specify the angle at which I want to look at the cube. In a $3$D setting I strongly prefer the interactive alternative.
Now is there a way to automatically add a continuous color legend to an rgl plot? If not, do you know why this hasn't been implemented? Or would you solve my problem completely different altogether?
P.S. sorry for the formatting, I'm new to SO and the math environment "$" doesn't seem to work here.
The reason this hasn't been implemented is because until fairly recently it wasn't easy to have a static legend and a dynamic plot in the same window.
Now it's easy; there's a legend3d() function that might do what you want, but I think you probably want a different sort of legend than it will draw. If you know how to draw what you want in 2D, you can use the bgplot3d() function to put it in the background of your plot.
Both of those options give bitmapped legends. It would also be possible to do vector-based legends, but that would be quite a bit more work.
I am trying to build an interactive plot. It has properties between a scatterplot and a network - I have a list of nodes and edges (network), but I also would like to constrain the nodes, sometimes on the x-axis sometimes on both x- and y- axis (scatterplot). Finally, I have a text label associated with each node that I would like to display (instead of a dot). I was able to create this using ggplot2.
However, some data sets are too large for this to work without the text labels from each node overlapping. Hence, I would now like to add an interactive feature so that the plot consists of dots representing each node, but that upon UI (such as hovering over a dot), the text label belonging to that dot will be revealed.
I would like to achieve this using R.
I tried animint (https://github.com/tdhock/animint) but it seems to mostly allow interaction between two plots, and here I would like to keep it all in one plot.
I also tried htmlwidgets (http://www.htmlwidgets.org/). I looked at two of their packages: I tried using metricsgraphics (mjs_plot), as it has a show_rollover_text option and mouseover option. However, this package does not allow combination of geoms, and so I could not have both dots (nodes) and lines (edges) represented. I also tried network3D package, but that seems to automatically position nodes so that they are distanced far away from each other, and does not seem to provide options to fix each node on a given x and y location.
I am just looking for advice on any other packages I should maybe consider to solve this problem and/or if I may be missing a feature from a package I already tried that could solve this problem. Thank you.
Maybe identify() will be useful for you. But it works only for base plotting system.
x <- rnorm(300)
y <- rnorm(300)
labs <- seq(300)
plot(x,y)
identify(x,y, labels = labs, plot=TRUE)
identify pic
I want to plot several lists of points, each list has distance (decimal) and error_no (1-8). So far I am using the following:
plot(b1$dist1, b1$e1, col="blue",type="p", pch=20, cex=.5)
points(b1$dist2, b1$e2, col="blue", pch=22)
to add them both to the same plot. (I will add legends, etc later on).
The problem I have is that points overlap, and even when changing the character using for plotting, it covers up previous points. Since I am planning on plotting a lot more than just 2 this will be a big problem.
I found some ways in:
http://www.rensenieuwenhuis.nl/r-sessions-13-overlapping-data-points/
But I would rather do something that would space the points along the y axis, one way would be to add .1, then .2, and so on, but I was wondering if there was any package to do that for me.
Cheers
M
ps: if I missed something, please let me know.
As noted in the very first point in the link you posted, jitter will slightly move all your points. If you just want to move the points on the y-axis:
plot(b1$dist1, b1$e1, col="blue",type="p", pch=20, cex=.5)
points(b1$dist2, jitter(b1$e2), col="blue", pch=22)
Depends a lot on what information you wish to impart to the reader of your chart. A common solution is to use the transparency quality of R's color specification. Instead of calling a color "blue" for example, set the color to #0000FF44 (Apologies if I just set it to red or green) The final two bytes define the transparency, from 00 to FF, so overlapping data points will appear darker than standalone points.
Look at the spread.labs function in the TeachingDemos package, particularly the example. It may be that you can use that function to create your plot (the examples deal with labels, but could just as easily be applied to the points themselves). The key is that you will need to find the new locations based on the combined data, then plot. If the function as is does not do what you want, you could still look at the code and use the ideas to spread out your points.
Another approach would be to restructure your data and use the ggplot2 package with "dodging". Other approaches rather than using points several times would be the matplot function, using the col argument to plot with a vector, or lattice or ggplot2 plots. You will probably need to restructure the data for any of these.