currently I am plotting 2000 some lines on a single plot in r. I am using the data from a spreadsheet which i cannot disclose due to sensitive information, but I'll try to illistrate how it is arranged.
x1/x1/x1/x1/x1/x1/etc.
y1/y1/y1/y1/y1/y1/etc.
x2/x2/x2/x2/x2/x2/etc.
y2/y2/y2/y2/y2/y2/etc.
...
x4436/x4436/x4436/etc.
y4436/y4436/y4436/etc.
where each x1,y1 is a point on a separate line. I need to plot a point on the endpoint of each line and I cannot seem to get my code to work. Currently I am using this to generate the points:
for (k in (1:2218)*2) {
q <- unlist(e_web_clear[2*k])
w <- unlist(e_web_clear[716])
points(w, q, col = "lightblue")
}
the way I imagined it, it would loop back to each point in every other row, to get only the y value for each line, and it would take the values from only the last column of my data (column 716).
needless to say, it did not work as intended, any suggestions?
EDIT:
spreadsheet with just a small portion of values here
and the code used to generate the lines:
for (j in (1:2218)*2) {
x <- unlist(e_web_clear[2*j-1,])
y <- unlist(e_web_clear[2*j,])
lines(x,y,'l',lwd=.00000000001, col="black")
}
data was imported as text file
Edit2:
this is the graph i am getting.
the graph i want to get would have the endpoint of each line highlighted in light blue. i believe it should look something like this. http: / /imgur.com/13b9MZL
figured it out.
I edited my line loop to place a point on the last vector point of each line.
for (j in (1:2218)*2) {
x <- unlist(e_web_clear[2*j-1,])
y <- unlist(e_web_clear[2*j,])
lines(x,y,'l',lwd=.00000000001, col="black")
points(x[358], y[358], lwd = 1.5, cex = .1, col = "lightblue")
}
Related
The code below plots 10 dots on the x-axis, one at a time. At any one point in time, the animation displays only one dot. I am looking to end up with a plot with all 10 dots. I would like the second dot to be added to the plot showing the first dot; the third to be added to the plot showing the first two dots, etc. I looked at the documentation for saveGIF for a parameter that would somehow cumulate the frames, but could not find a relevant parameter there. It looks like it should be possible. Yihui Xie, the creator of the animation package, did exactly that in the top right plot of this example https://yihui.org/animation/example/buffon-needle/
library(animation)
saveGIF({
for (i in 1:10) {
x <- rnorm(1,0,1)
plot(x,0,xlim=c(0,1),ylim=c(-1,1))
}
})
You can generate the 10 numbers in advance, and plot them incrementally, e.g.,
library(animation)
saveGIF({
n <- 10
x <- rnorm(n, 0, 1)
for (i in seq_len(n)) {
plot(head(x, i), 0, xlim = c(1, n), ylim = c(-1, 1))
}
})
I created a for loop to plot 38 lines (which are the rows of my matrix, results.summary.evap, and correspond to 38 total samples). I'd like to make these lines different colors, based on a characteristic pertaining to each sample: age. I can access the age in my input matrix: surp.data$Age_ka.
However, the matrix I am looping over (results.summary.evap) does not have sample age or sample name, though each sample should be located in the same rows for both surp.data and results.summary.evap.
Here is the for loop I created to plot 38 lines, one corresponding to each sample. In this case, results.summary.evap is what I am plotting from, and this matrix is derived from information in the surp.data input file.
par(mfrow=c(3,1))
par(mar=c(3, 4, 2, 0.5))
plot(NA,NA,xlim=c(0,10),ylim=c(0,2500), ylab = "Evaporation (mm/yr)", xlab = "Relative Humidity")
for(i in 1:range){
lines(rh.sens,results.summary.evap[i,])
}
```
I'd like to plot lines in different colors based on the age associated with each sample. I tried to incorporate an if/else statement into the loop, that would plot in a different color if the corresponding sample age was greater that 20 in the input file.
```
for(i in 1:range){
if surp.data$Age_ka[i]>20 {
lines(rh.sens,results.summary.evap[i,], col = 'red')
} else {
lines(rh.sens,results.summary.evap[i,], col = 'black')
}
}
This for loop won't run (due to issues with parentheses). I'm not sure if what I am doing if fundamentally wrong, or if i've just missed a parenthesis somewhere. I'm also not sure how to make this a bit more robust; for example, by plotting in 6-8 different colors based on age ranges, rather than just two.
Thank you!
You're missing parenthesis around your if statement
for(i in 1:range){
if(surp.data$Age_ka[i]>20){
lines(rh.sens,results.summary.evap[i,], col = 'red')
} else {
lines(rh.sens,results.summary.evap[i,], col = 'black')
}
}
I'm still relatively inexperienced manipulating plots in R, and am in need of assistance. I ran a redundancy analysis in R using the rda() function, but now I need to simplify the figure to exclude unnecessary information. The code I'm currently using is:
abio1516<-read.csv("1516 descriptors.csv")
attach(abio1516)
bio1516<-read.csv("1516habund.csv")
attach(bio1516)
rda1516<-rda(bio1516[,2:18],abio1516[,2:6])
anova(rda1516)
RsquareAdj(rda1516)
summary(rda1516)
varpart(bio1516[,2:18],~Distance_to_source,~Depth, ~Veg._cover, ~Surface_area,data=abio1516)
plot(rda1516,bty="n",xaxt="n",yaxt="n",main="1516; P=, R^2=",
ylab="Driven by , Var explained=",xlab="Driven by , Var explained=")
The produced plot looks like this:
Please help me modify my code to: exclude the sites (sit#), all axes, and the internal dashed lines.
I'd also like to either expand the size of the field, or move the vector labels to all fit in the plotting field.
updated as per responses, working code below this point
plot(rda,bty="n",xaxt="n",yaxt="n",type="n",main="xxx",ylab="xxx",xlab="xxx
Overall best:xxx")
abline(h=0,v=0,col="white",lwd=3)
points(rda,display="species",col="blue")
points(rda,display="cn",col="black")
text(rda,display="cn",col="black")
Start by plotting the rda with type = "n" which generates an empty plot to which you can add the things you want. The dotted lines are hard coded into the plot.cca function, so you need either make your own version, or use abline to hide them (then use box to cover up the holes in the axes).
require(vegan)
data(dune, dune.env)
rda1516 <- rda(dune~., data = dune.env)
plot(rda1516, type = "n")
abline(h = 0, v = 0, col = "white", lwd = 3)
box()
points(rda1516, display = "species")
points(rda1516, display = "cn", col = "blue")
text(rda1516, display = "cn", col = "blue")
If the text labels are not in the correct position, you can use the argument pos to move them (make a vector as long as the number of arrows you have with the integers 1 - 4 to move the label down, left, up, or right. (there might be better solutions to this)
I apologize first for bringing what I imagine to be a ridiculously simple problem here, but I have been unable to glean from the help file for package 'polynom' how to solve this problem. For one out of several years, I have two vectors of x (d for day of year) and y (e for an index of egg production) data:
d=c(169,176,183,190,197,204,211,218,225,232,239,246)
e=c(0,0,0.006839425,0.027323127,0.024666883,0.005603878,0.016599262,0.002810977,0.00560387 8,0,0.002810977,0.002810977)
I want to, for each year, use the poly.calc function to create a polynomial function that I can use to interpolate the timing of maximum egg production. I want then to superimpose the function on a plot of the data. To begin, I have no problem with the poly.calc function:
egg1996<-poly.calc(d,e)
egg1996
3216904000 - 173356400*x + 4239900*x^2 - 62124.17*x^3 + 605.9178*x^4 - 4.13053*x^5 +
0.02008226*x^6 - 6.963636e-05*x^7 + 1.687736e-07*x^8
I can then simply
plot(d,e)
But when I try to use the lines function to superimpose the function on the plot, I get confused. The help file states that the output of poly.calc is an object of class polynomial, and so I assume that "egg1996" will be the "x" in:
lines(x, len = 100, xlim = NULL, ylim = NULL, ...)
But I cannot seem to, based on the example listed:
lines (poly.calc( 2:4), lty = 2)
Or based on the arguments:
x an object of class "polynomial".
len size of vector at which evaluations are to be made.
xlim, ylim the range of x and y values with sensible defaults
Come up with a command that successfully graphs the polynomial "egg1996" onto the raw data.
I understand that this question is beneath you folks, but I would be very grateful for a little help. Many thanks.
I don't work with the polynom package, but the resultant data set is on a completely different scale (both X & Y axes) than the first plot() call. If you don't mind having it in two separate panels, this provides both plots for comparison:
library(polynom)
d <- c(169,176,183,190,197,204,211,218,225,232,239,246)
e <- c(0,0,0.006839425,0.027323127,0.024666883,0.005603878,
0.016599262,0.002810977,0.005603878,0,0.002810977,0.002810977)
egg1996 <- poly.calc(d,e)
par(mfrow=c(1,2))
plot(d, e)
plot(egg1996)
I need to draw lines from the data stored in a text file.
So far I am able only to draw points on a graph and i would like to have them as lines (line graph).
Here's the code:
pupil_data <- read.table("C:/a1t_left_test.dat", header=T, sep="\t")
max_y <- max(pupil_data$PupilLeft)
plot(NA,NA,xlim=c(0,length(pupil_data$PupilLeft)), ylim=c(2,max_y));
for (i in 1:(length(pupil_data$PupilLeft) - 1))
{
points(i, y = pupil_data$PupilLeft[i], type = "o", col = "red", cex = 0.5, lwd = 2.0)
}
Please help me change this line of code:
points(i, y = pupil_data$PupilLeft[i], type = "o", col = "red")
to draw lines from the data.
Here is the data in the file:
PupilLeft
3.553479
3.539469
3.527239
3.613131
3.649437
3.632779
3.614373
3.605981
3.595985
3.630766
3.590724
3.626535
3.62386
3.619688
3.595711
3.627841
3.623596
3.650569
3.64876
By default, R will plot a single vector as the y coordinates, and use a sequence for the x coordinates. So to make the plot you are after, all you need is:
plot(pupil_data$PupilLeft, type = "o")
You haven't provided any example data, but you can see this with the built-in iris data set:
plot(iris[,1], type = "o")
This does in fact plot the points as lines. If you are actually getting points without lines, you'll need to provide a working example with your data to figure out why.
EDIT:
Your original code doesn't work because of the loop. You are in effect asking R to plot a line connecting a single point to itself each time through the loop. The next time through the loop R doesn't know that there are other points that you want connected; if it did, this would break the intended use of points, which is to add points/lines to an existing plot.
Of course, the line connecting a point to itself doesn't really make sense, and so it isn't plotted (or is plotted too small to see, same result).
Your example is most easily done without a loop:
PupilLeft <- c(3.553479 ,3.539469 ,3.527239 ,3.613131 ,3.649437 ,3.632779 ,3.614373
,3.605981 ,3.595985 ,3.630766 ,3.590724 ,3.626535 ,3.62386 ,3.619688
,3.595711 ,3.627841 ,3.623596 ,3.650569 ,3.64876)
plot(PupilLeft, type = 'o')
If you really do need to use a loop, then the coding becomes more involved. One approach would be to use a closure:
makeaddpoint <- function(firstpoint){
## firstpoint is the y value of the first point in the series
lastpt <- firstpoint
lastptind <- 1
addpoint <- function(nextpt, ...){
pts <- rbind(c(lastptind, lastpt), c(lastptind + 1, nextpt))
points(pts, ... )
lastpt <<- nextpt
lastptind <<- lastptind + 1
}
return(addpoint)
}
myaddpoint <- makeaddpoint(PupilLeft[1])
plot(NA,NA,xlim=c(0,length(PupilLeft)), ylim=c(2,max(PupilLeft)))
for (i in 2:(length(PupilLeft)))
{
myaddpoint(PupilLeft[i], type = "o")
}
You can then wrap the myaddpoint call in the for loop with whatever testing you need to decide whether or not you will actually plot that point. The function returned by makeaddpoint will keep track of the plot indexing for you.
This is normal programming for Lisp-like languages. If you find it confusing you can do this without a closure, but you'll need to handle incrementing the index and storing the previous point value 'manually' in your loop.
There is a strong aversion among experienced R coders to using for-loops when not really needed. This is an example of a loop-less use of a vectorized function named segments that takes 4 vectors as arguments: x0,y0, x1,y1
npups <-length(pupil_data$PupilLeft)
segments(1:(npups-1), pupil_data$PupilLeft[-npups], # the starting points
2:npups, pupil_data$PupilLeft[-1] ) # the ending points