Sometimes we make plotting functions that alter graphical parameters, par. For instance if I want to combine base and grid I need to do some magic that alters par. Now I want to allow users to plot with such a function and not have the side effects in the next call to the same function. For example the following function if pressed twice results in the following two images each time:
library(ggplot2); library(grid); library(gridBase)
plotter <- function(){
#invisible(try(dev.off()))
layout(matrix(c(1, 2), nrow = 1, byrow = TRUE))
#Draw base plot
plot.new()
graphics::par(mar=c(1, 1, 1, 1), new = TRUE)
plot(1:10)
#Draw ggplot
plot.new()
vps <- baseViewports()
print( ggplot(mtcars, aes(mpg, hp)) + geom_point(), vp = vpStack(vps$figure,vps$plot))
}
plotter()
plotter()
Notice the smushed ggplot the second go round. Now I could fix this by uncommenting out the line invisible(try(dev.off())). But...when I then want to plot to an external device the call to pdf for example below, gets turned off. How can I restart the interactive device safely, or some other answer as I may be asking the wrong question.
pdf("test.pdf")
plotter()
dev.off()
I tried adding .pardefault <- par(no.readonly = T) at the beginning of the function call and par(.pardefault) at the end via: https://stackoverflow.com/a/9292673/1000343 but this does not work. This answer https://stackoverflow.com/a/5790430/1000343 does not work either.
Perhaps there's a way to use dev.cur against a list of internal plot devices to recognize if the plot device is RStudio or windows or such and only restart in those cases.
Related
Why does this happen?
plot(x,y)
yx.lm <- lm(y ~ x)
lines(x, predict(yx.lm), col="red")
Error in plot.xy(xy.coords(x, y), type = type, ...) :
plot.new has not been called yet
Some action, very possibly not represented in the visible code, has closed the interactive screen device.
It could be done either by a "click" on a close-button, or it could also be done by an extra dev.off() when plotting to a file-graphics device. (The second possibility might happen if you paste in a multi-line plotting command that has a dev.off() at the end of it, but had errored out at the opening of the external device. So the dangling dev.off() on a separate line accidentally closes the interactive device).
Some (most?) R implementations will start up a screen graphics device open automatically, but if you close it down, you then need to re-initialize it.
On Windows that might be window(); on a Mac, quartz(); and on a Linux box, x11(). You also may need to issue a plot.new() command. I just follow orders. When I get that error I issue plot.new() and if I don't see a plot window, I issue quartz() as well. I then start over from the beginning with a new plot(., ., ...) command and any further additions to that plot screen image.
In my case, I was trying to call plot(x, y) and lines(x, predict(yx.lm), col="red") in two separate chunks in Rmarkdown file. It worked without problems when running chunk by chunk, but the corresponding document wouldn't knit. After I moved all plotting calls within one chunk, problem was resolved.
As a newbie, I faced the same 'problem'.
In newbie terms :
when you call plot(), the graph window gets the focus and you cannot enter further commands into R. That is when you conclude that you must close the graph window to return to R.
However, some commands, like identify(), act on open/active graph windows.
When identify() cannot find an open/active graph window, it gives this error message.
However, you can simply click on the R window without closing the graph window. Then you can type more commands at the R prompt, like identify() etc.
plot.new() error occurs when only part of the function is ran.
Please find the attachment for an example to correct error
With error....When abline is ran without plot() above
Error-free ...When both plot and abline ran together
I had the same problem... my problem was that I was closing my quartz window after plot(x,y). Once I kept it open, the lines that previously resulted in errors just added things to my plot (like they were supposed to). Hopefully this might help some people who arrive at this page.
If someone is using print function (for example, with mtext), then firstly depict a null plot:
plot(0,type='n',axes=FALSE,ann=FALSE)
and then print with newpage = F
print(data, newpage = F)
I had the problem in an RMarkdown, and putting the offending line on the previous line of code helped.
Minimal Reproducible Example
This will error if run line by line in an Rmd:
x <- rbind(matrix(rnorm(100, sd = 0.3), ncol = 2),
matrix(rnorm(100, mean = 1, sd = 0.3), ncol = 2))
colnames(x) <- c("x", "y")
(cl <- kmeans(x, 2))
plot(x, col = cl$cluster)
points(cl$centers, col = 1:2, pch = 8, cex = 2)
but this works:
x <- rbind(matrix(rnorm(100, sd = 0.3), ncol = 2),
matrix(rnorm(100, mean = 1, sd = 0.3), ncol = 2))
colnames(x) <- c("x", "y")
(cl <- kmeans(x, 2))
plot(x, col = cl$cluster); points(cl$centers, col = 1:2, pch = 8, cex = 2)
The only change is that the offending line (the last one) is placed after the last succeeding line (placing a ; in between). You can do it for as many offending lines as desired.
I know similar questions have been already asked so sorry if this is a redundant question! However, I can't seem to find a solution that arranges several ggplots from a list onto 1 page over several pages.
I have a list of approximately 100 ggplots - I want to plot every 4 ggplots on 1 page, and iterate through the list until all the ggplots have been plotted. I then want to export the approximately 25 pages to a single pdf file.
So far, I've tried:
pdf("plots.pdf", onefile = TRUE, width = 11, height = 8.5)
for (i in 0:24) {
ggarrange(list[[4i+1]], list[[4i+2]], list[[4i+3]], list[[4i+4]],
nrow = 2, ncol = 2, common.legend = TRUE, legend = 'bottom'
}
dev.off()
However, I'm getting the error that the subscript is out of bounds. I've tried narrowing the range in the for loop to try to overcome this error but it's returning the same error. I also know we can use marrangeGrob(), but I can't seem to add a common legend to the file.
Really appreciate any help!
It would be helpful if you could provide some small list of plots to test on.
I have tried to recreate your scenario, and have found that it wasn't working unless I explicitly print the ggarrange object.
plot <- ggplot(mtcars, aes(x = cyl, y = mpg)) +
geom_point()
plot_list <- list(plot, plot, plot, plot, plot, plot, plot, plot)
pdf("test.pdf", 11, 8.5)
for(i in 0:3){
print(ggarrange(plot_list[[2*i + 1]], plot_list[[2*i + 1]], nrow = 2, ncol = 1))
}
dev.off()
This worked for me. Noting akrun's comment that you forgot your * symbol.
I am trying to create and record plots in a 1x1 device:
par(mfrow = c(1, 1) )
plot(rnorm(10) )
p1 <- recordPlot()
plot(rnorm(20) )
p2 <- recordPlot()
and then to put them in a new layout (e.g., a 1x2 device):
par(mfrow = c(1, 2) )
p1
p2
However, this produce the same effect (i.e., plotting each plot in a 1x1 device). It seems replaying plots uses the original layout (graphical parameters) that was in effect when they were recorded.
Is there some method that allows a saved plot to be replayed in a new layout ?
NB: I am aware this would be easier via ggplot2, but my question is about base plots.
I did some digging, and I don't think this is possible. I used the following to look at what attributes are available inside the object. None of them seemed to indicate the layout could be adjusted.
summary(p1)
p1[[1]]
p1[[2]]
If you need the same plot across two different layouts could you use set.seed() to recreated the same plot? See the example below.
par(mfrow = c(1, 1))
set.seed(1234)
plot(rnorm(10))
par(mfrow = c(1, 2))
set.seed(1234)
plot(rnorm(10))
I'd be interested to see if anyone else has a better answer!
I've been trying to draw two plots using R's ggplot library in RStudio. Problem is, when I draw two within one function, only the last one displays (in RStudio's "plots" view) and the first one disappears. Even worse, when I run ggsave() after each plot - which saves them to a file - neither of them appear (but the files save as expected). However, I want to view what I've saved in the plots as I was able to before.
Is there a way I can both display what I'll be plotting in RStudio's plots view and also save them? Moreover, when the plots are not being saved, why does the display problem happen when there's more than one plot? (i.e. why does it show the last one but not the ones before?)
The code with the plotting parts are below. I've removed some parts because they seem unnecessary (but can add them if they are indeed relevant).
HHIplot = ggplot(pergame)
# some ggplot geoms and misc. here
ggsave(paste("HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
HHIAvePlot = ggplot(AveHHI, aes(x = AveHHI$n_brokers))
# some ggplot geoms and misc. here
ggsave(paste("Average HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
I've already taken a look here and here but neither have helped. Adding a print(HHIplot) or print(HHIAvePlot) after the ggsave() lines has not displayed the plot.
Many thanks in advance.
Update 1: The solution suggested below didn't work, although it works for the answer's sample code. I passed the ggplot objects to .Globalenv and print() gives me an empty gray box on the plot area (which I imagine is an empty ggplot object with no layers). I think the issue might lie in some of the layers or manipulators I have used, so I've brought the full code for one ggplot object below. Any thoughts? (Note: I've tried putting the assign() line in all possible locations in relation to ggsave() and ggplot().)
HHIplot = ggplot(pergame)
HHIplot +
geom_point(aes(x = pergame$n_brokers, y = pergame$HHI)) +
scale_y_continuous(limits = c(0,10000)) +
scale_x_discrete(breaks = gameSizes) +
labs(title = paste("HHI Index of all games,",year,"Finals"),
x = "Game Size", y = "Herfindahl-Hirschman Index") +
theme(text = element_text(size=15),axis.text.x = element_text(angle = 0, hjust = 1))
assign("HHIplot",HHIplot, envir = .GlobalEnv)
ggsave(paste("HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
I'll preface this by saying that the following is bad practice. It's considered bad practice to break a programming language's scoping rules for something as trivial as this, but here's how it's done anyway.
So within the body of your function you'll create both plots and put them into variables. Then you'll use ggsave() to write them out. Finally, you'll use assign() to push the variables to the global scope.
library(ggplot2)
myFun <- function() {
#some sample data that you should be passing into the function via arguments
df <- data.frame(x=1:10, y1=1:10, y2=10:1)
p1 <- ggplot(df, aes(x=x, y=y1))+geom_point()
p2 <- ggplot(df, aes(x=x, y=y2))+geom_point()
ggsave('p1.jpg', p1)
ggsave('p2.jpg', p2)
assign('p1', p1, envir=.GlobalEnv)
assign('p2', p2, envir=.GlobalEnv)
return()
}
Now, when you run myFun() it will write out your two plots to .jpg files, and also drop the plots into your global environment so that you can just run p1 or p2 on the console and they'll appear in RStudio's Plot pane.
ONCE AGAIN, THIS IS BAD PRACTICE
Good practice would be to not worry about the fact that they're not popping up in RStudio. They wrote out to files, and you know they did, so go look at them there.
I’d really appreciate your help with the following problem. I know several ways to save a single plot to a file. My question is: How do I correctly save a multiplot to a file?
To begin with, I’m not an experienced R user. I use ggplot2 to create my plots, and another thing I should probably mention is that I use the RStudio GUI. Using an example from the R Cookbook, I'm able to create multiple plots in one window.
I would like to save this so-called multiplot to a file (preferably as jpeg), but somehow fail to do this.
I’m creating the multiplot as follows:
##define multiplot function
multiplot <- function(..., plotlist=NULL, cols) {
require(grid)
# Make a list from the ... arguments and plotlist
plots <- c(list(...), plotlist)
numPlots = length(plots)
# Make the panel
plotCols = cols # Number of columns of plots
plotRows = ceiling(numPlots/plotCols) # Number of rows needed, calculated from # of cols
# Set up the page
grid.newpage()
pushViewport(viewport(layout = grid.layout(plotRows, plotCols)))
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
# Make each plot, in the correct location
for (i in 1:numPlots) {
curRow = ceiling(i/plotCols)
curCol = (i-1) %% plotCols + 1
print(plots[[i]], vp = vplayout(curRow, curCol ))
}
}
## define subplots (short example here, I specified some more aesthetics in my script)
plot1a <- qplot(variable1,variable2,data=Mydataframe1)
plot1b <- qplot(variable1,variable3,data=Mydataframe1)
plot1c <- qplot(variable1,variable2,data=Mydataframe2)
plot1d <- qplot(variable1,variable3,data=Mydataframe2)
## plot in one frame
Myplot <- multiplot(plot1a,plot1b,plot1c,plot1d, cols=2)
This gives the desired result. The problem arises when I try to save to a file. I can do this manually in RStudio (using Export -> Save plot as image), but I would like to run everything in a script. I manage to save only subplot1d (which is last_plot()), and not the complete multiplot.
What I’ve tried so far:
Using ggsave
ggsave(filename = "D:/R/plots/Myplots.jpg")
This results in only subplot 1d being saved.
Using jpeg(), print() and dev.off()
jpeg(filename = "Myplot.jpg", pointsize =12, quality = 200, bg = "white", res = NA, restoreConsole = TRUE)
print(Myplot)
dev.off()
This results in a completely white image (just the background I assume). print(Myplot) returns NULL.
Not sure what I’m doing wrong here. My lack of understanding R is the reason I am stuck trying to find a solution. Can anyone explain what I’m doing wrong and perhaps suggest a way to solve my problem(s)?
Its because Myplot is the returned value from your multiplot function, and it returns nothing (its job is to print the graphs). You need to call multiplot with the jpeg device open:
jpeg(filename = "Myplot.jpg", pointsize =12, quality = 200, bg = "white", res = NA, restoreConsole = TRUE)
multiplot(plot1a,plot1b,plot1c,plot1d, cols=2)
dev.off()
should work.
Using the example code (R cookbook), it works for me
png("chickweight.png")
multiplot(p1, p2, p3, p4, cols=2)
dev.off()
And for completeness sake, ggsave does not work as it only saves the last printed ggplot object, which in your case is just the last plot. This is caused by the fact that multiplot creates the plot by drawing the ggplot objects onto different subsets of the total graphics device. An alternative is to create the plot by combining the ggplot objects into one big ggplot object, and then printing the object. This would be compatible with ggsave. This approach is implemented by arrangeGrob in the gridExtra package.