I am running R in jupyter, but I am running across some issues with plotting. Specifically whenever I plot the returned plotting window takes up the entire screen. I tried changing the dimension of the plot in R with par(pin=c(1,1)) etc... and it shrunk the actual image of the plot, but the cell width the images is in still takes up the entire screen. I can zoom out in my browser, but then I can't see my lines of code.
Code:
x <- runif(100)
hist(x)
Any suggestions on how to fix this would be appreciated. Thanks.
P.S. I would post an image, but I just created this account and need at least 10 rep points to post images
Answer:
I was able to change the options with the code below so my plots looked a little bit more reasonable
options(repr.plot.height=3)
options(repr.plot.width=3)
I am trying to have a nice looking plot for two (or possibly more) continuous values in the form of a pie chart using ggplot2.
The code is the following :
library("ggplot2")
library("ggthemes") ## for theme_economist
df <- data.frame(origin=c('with','without'),value=c(24536,50456))
pie <- ggplot(df, aes(x = "",y=value, fill = origin))+
geom_bar(width = 1,stat="identity")+
coord_polar(theta = "y",start=pi/3)+
theme_economist()
The pie is relatively fine except that the contours of the pie seems to be a bit irregularly drawn.Of course when you export it as a pdf it looks fine but displayed in RStudio or Shiny it doesn't look nice at all.
Is there a way to change the resolution of the ggplot object directly or to make renderplot() aware that we want to display the image at a high resolution ?
I tried modifying the res argument of the renderPlot() function but it distorts the image and do not get rid of the irregularity of the border.
How to make the contours of the pie smoother on Shiny or RStudio directly ? Thanks.
To improve the resolution of the plot on Shiny you have to set the res argument to its default value of 72. It does not make a lot of sense to me but it worked just fine the resolution went from really bad to really nice !
However increasing its value further can lead to distortion of the image.
It seems that for now you cannot change the resolution of the plotting object itself before exporting it or rendering it into Shiny.
I am experimenting with the investigate_var_importance in package of bartMachine
investigate_var_importance(bart_machine_cv, num_replicates_for_avg = 20)
It turns out that the generated graph is so big, especially the text label along with the x-axis. The default [R Graphics: Device 2(Active) cannot even hold the whole picture. How to change the font size and margin of this plot?
margin can be set by par(mar=c(bottomMargin, left, up, right))
see par to set that parameter
c(0,0,0,0) will not leave any space. You might not want this, as there wouldn't be any space for the axis.
par(oma=c(bottomMargin, left, up, right))
sets the outer margins of the plot
if you send the plot to a pdf, you can increase the size of the plot, which will be able to hold the whole plot i.e,
pdf('nameOfplot.pdf', 20, 6) ## opens a device, and produces a file much wider than longer
plot whater you want
dev.off() ## closes the device you have opened with pdf
if you play with those parameters you might be able to fit your plot
I recently installed ggplot2 and tried a qplot. The plot comes out like this,
If you notice you can see that the markers seem to look deformed rather than circles. Is there a way to correct this?
Here is my code:
require(ggplot2)
set.seed(1410)
qplot(carat, price, data = diamonds)
EDIT: The plot looks fine when exported to a pdf.
I am using R3.0.2 ggplot2_0.9.3.1 on elementary OS.Thanks.
I usually don't worry about the look of the picture in the "window view" / "r view" -- it is just a graphical view of what the picture will look given the current setting for the resolution.
If possible, I save a picture as an eps or pdf file. They are vector based picture and scale well regardless of size.
If I don't use an eps or pdf file, I use png files to save my pictures:
g1 <- ggplot(data, aes(x=X1, y=Y1)+
geom_point(x)
png("high_res_png.png", width = 10000, height = 7000, res = 1300)
print(g1)
dev.off()
Using a lot of pixels on a png will prevent the "saved" picture from looking "fuzzy" or "oddly" shaped (the size of it will be large, but the png looks good even when you zoom in). Hope that helps.
The goofy looking circles is an artifact of your window system; on my Mac OS X (Quartz) setup, default qplot gives great-looking circles. However, I recall that the points do look a little like yours on my Linux box at home...
Shape is customizable, though. The following gives squares rotated 45 degrees, for instance:
qplot(carat, price, data = diamonds) + scale_shape_identity() + geom_point(shape = 23)
I'm new to R but I've made numerous correlation plots with smaller data sets. However, when I try to plot a large dataset (2gb+), I can produce the plot just fine, but the legend doesn't show up. Any advice? or alternatives?
library(gplots)
r.cor <- cor(r)
layout(matrix(c(1,1,1,1,1,1,1,1,2,2), 5, 2, byrow = TRUE))
par(oma=c(5,7,1,1))
cx <- rev(colorpanel(25,"yellow","black","blue"))
leg <- seq(min(r.cor,na.rm=T),max(r.cor,na.rm=T),length=10)
image(r.cor,main="Correlation plot Normal/Tumor data",axes=F,col=cx)
axis(1, at=seq(0,1,length=ncol(r.cor)), labels=dimnames(r.cor)[[2]],
cex.axis=0.9,las=2)
axis(2,at=seq(0,1,length=ncol(r.cor)), labels=dimnames(r.cor)[[2]],
cex.axis=0.9,las=2)
image(as.matrix(leg),col=cx,axes=T)
Error in plot.new() : figure margins too large
tmp <- round(leg,2)
axis(1,at=seq(0,1,length=length(leg)), labels=tmp,cex.axis=1)
This error can occur in Rstudio simply because your "Plots" pane is just barely too small. Try zooming your "Files, Plots, Packages, Help, Viewer" and see if it helps!
The problem is that the small figure region 2 created by your layout() call is not sufficiently large enough to contain just the default margins, let alone a plot.
More generally, you get this error if the size of the plotting region on the device is not large enough to actually do any plotting. For the OP's case the issue was having too small a plotting device to contain all the subplots and their margins and leave a large enough plotting region to draw in.
RStudio users can encounter this error if the Plot tab is too small to leave enough room to contain the margins, plotting region etc. This is because the physical size of that pane is the size of the graphics device. These are not independent issues; the plot pane in RStudio is just another plotting device, like png(), pdf(), windows(), and X11().
Solutions include:
reducing the size of the margins; this might help especially if you are trying, as in the case of the OP, to draw several plots on the same device.
increasing the physical dimensions of the device, either in the call to the device (e.g. png(), pdf(), etc) or by resizing the window / pane containing the device
reducing the size of text on the plot as that can control the size of margins etc.
Reduce the size of the margins
Before the line causing the problem try:
par(mar = rep(2, 4))
then plot the second image
image(as.matrix(leg),col=cx,axes=T)
You'll need to play around with the size of the margins on the par() call I show to get this right.
Increase the size of the device
You may also need to increase the size of the actual device onto which you are plotting.
A final tip, save the par() defaults before changing them, so change your existing par() call to:
op <- par(oma=c(5,7,1,1))
then at the end of plotting do
par(op)
If you get this message in RStudio, clicking the 'broomstick' figure "Clear All Plots" in Plots tab and trying plot() again may work.
This sometimes happen in RStudio. In order to solve it you can attempt to plot to an external window (Windows-only):
windows() ## create window to plot your file
## ... your plotting code here ...
dev.off()
I got this error in R Studio, and was simply fixed by making the sidebar bigger by clicking and dragging on its edge from right to left.
Picture here: https://janac.medium.com/error-in-plot-new-figure-margins-too-large-in-r-214621b4b2af
Check if your object is a list or a vector. To do this, type is.list(yourobject). If this is true, try renaming it x<-unlist(yourobject). This will make it into a vector you can plot.
Just zoom this area if you use RStudio.
I found this error today. Initially, I was trying to output it to a .jpeg file with low width and height.
jpeg("method1_test.jpg", width=900, height=900, res=40)
Later I increased the width and height to:
jpeg("method1_test.jpg", width=1900, height=1900, res=40)
The error was not there. :)
You can also play with the resolution, if the resolution is high, you need more width and height.
I had this error when I was trying to plot high dimensional data. If that's what is going on with you, try multidimensional scaling: http://www.statmethods.net/advstats/mds.html
I struggled with this error for weeks (using RStudio). I tried moving the plot window bigger and smaller, but that did not consistently help. When I moved (dragged) the application to my bigger monitor, the problem disappeared! I was stunned... so many wasted hours... I knew my code was correct...
If margin is low, then it is always better to start with new plotting device:
dev.new()
# plot()
# save your plot
dev.off()
You will never get margin error, unless you plot something large which can not be accommodated.
RStudio Plots canvas is limiting the plot width and heights. However if you make your plot from Rmarkdown code chunk, it works without canvas field limitation because plotting area set according to the paper size.
For instance:
```{r}
#inside of code chunk in Rmarkdown
grid <- par(mfrow=c(4, 5))
plot(faithful, main="Faithful eruptions")
plot(large.islands, main="Islands", ylab="Area")
...
par(grid)
```
I found the same error today. I have tried the "Clear all Plots" button, but it was giving me the same error. Then this trick worked for me,
Try to increase the plot area by dragging. It will help you for sure.
I have just use the Clear all plots then again give the plot command and it was helpfull