How can I export multiple plots as a pdf in R ?
Does anyone know What is the command for this ?
You may want to try this:
pdf(file='plot.pdf')
plot(1:10)
dev.off()
Since you didn't provide any reproducible example I just give you the example written above. See the documentation by doing ?pdf and ?dev.off()
Multiple plots would be (adding to Jilber)
pdf(file='plot.pdf')
par(mfrow=(c(1,3)))
plot(1:10)
plot(rnorm(10)
plot(rnorm(10)
dev.off()
or You can use the plyr package to create a pdf with multiple plots
library(ply)
pdf("plots.pdf", width = 7, height = 7)
d_ply(df, .(z), failwith(NA, function(x){plot(x$y,main=unique(z))}), .print=TRUE)
dev.off()
were df is a data frame containing a conditional factor (z) and a target variable (y). You will get as many plots as z levels, all included in a pdf report.
The above answers will help you to export the plots in table but if you want them to be in table like 2-3 graphs in 1 row, you can use following code:
pdf("Export_Plots.pdf", width = 16 , height = 10, title = "EDA Plots for data")
par(mfrow=c(2,2))
for(i in 1:10){
par(mar = c(5,4,4,5)+.1)
plot(i)
}
dev.off()
Please check below link for more detail:
https://topbullets.com/2017/04/19/exporting-multiple-graphs-in-same-plot-to-pdf-in-r-topbullets-com/
Related
I have 2 ggplots: plot1 and plot2
When I show them in R using:
multi.page <- ggarrange(plot1, plot2,
nrow = 1, ncol = 1)
I get the overlap, but when I then want to safe this overlapping images as PDF it is not possible:
ggsave('/path/image.pdf',plot=multi.page,width=8,height=5)
Does anyone know a way?
Maybe with ggplot_add?
Thank you!
Instead of using ggsave, you could use the pdf device directly:
pdf('/path/image.pdf')
print(multi.page)
dev.off()
And you will have a pdf with your two plots on separate pages.
I have created one function that contains two types of plots and it will give you one image. However, the title of this image will change depending on one list, so, you will have several plots but different title.
(The original function will change the numbers that the plot uses but, in essence, is what I need).
This is the example that I have created.
list_genes <- c("GEN1", "GEN2", "GEN3")
myfunction <- function(x,y){
for(gene in list_genes){
# This to draw both plots
par(mfrow=c(2,1))
plot(x,y, main=paste0("Plot of ", gene))
hist(x, main=paste0("Plot of ", gene))
}
}
myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
Since the list has 3 elements, we get 3 plots.
However, as I need to create a presentation with all the plots that I generate, I found this post with a solution to create slides for several plots inside a for loop. It is what I want, but for that, I need to save my plots into a list/variable.
object <- myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
> object
NULL
I found this post (which gives you an interesting solution) but, the plots still cannot be saved into an object.
calling_myfunc <- function(){
myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
}
calling_myfunc()
object <- calling_myfunc()
> object
NULL
My final objective is to create a presentation (automatically) with all of the plots that I generate from my function. As I saw in this post. But I need to save the plots into a variable.
Could anyone help me with this?
Thanks very much in advance
Although I couldn't find the way to save the plots into an object, I found a way to create a presentation with those images thanks to this post and the export package.
library(export)
list_genes <- c("GEN1", "GEN2", "GEN3")
myfunction <- function(x,y){
for(gene in list_genes){
# This to draw both plots
par(mfrow=c(2,1))
plot(x,y, main=paste0("Plot of ", gene))
hist(x, main=paste0("Plot of ", gene))
graph2ppt(file="plots.pptx", width=6, height=5,append=TRUE) } }
myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
Of course, the width and height of the plots can be changed or put them as a parameter in the function.
Since the package is not available in CRAN for my current R version (4.1.2), I downloaded it from GitHub:
devtools::install_github("tomwenseleers/export")
In addition, I have found another package that I can use for the same purpose (although it adds one extra slide at the beginning, I don't know why)
library(eoffice)
list_genes <- c("GEN1", "GEN2", "GEN3")
myfunction <- function(x,y){
for(gene in list_genes){
# This to draw both plots
par(mfrow=c(2,1))
plot(x,y, main=paste0("Plot of ", gene))
hist(x, main=paste0("Plot of ", gene))
topptx(file="plots.pptx", width=6, height=5,append=TRUE)
}
}
myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
PS: I found the solution to create a presentation --> How to create a presentation in R with several plots obtained by a function?
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'm attempting to step through a dataset and create a histogram and summary table for each factor and save the output as a .svg . The histogram is created using ggplot2 and the summary table using summary().
I have successfully used the code below to save the output to a single .pdf with each page containing the relevant histogram/table. However, when I attempt to save each histogram/table combo into a set of .svg images using ggsave only the ggplot histogram is showing up in the .svg. The table is just white space.
I've tried using dev.copy Cairo and svg but all end up with the same result: Histogram renders, but table does not. If I save the image as a .png the table shows up.
I'm using the iris data as a reproducible dataset. I'm not using R-Studio which I saw was causing some "empty plot" grief for others.
#packages used
library(ggplot2)
library(gridExtra)
library(gtable)
library(Cairo)
#Create iris histogram plot
iris.hp<-ggplot(data=iris, aes(x=Sepal.Length)) +
geom_histogram(binwidth =.25,origin=-0.125,
right = TRUE,col="white", fill="steelblue4",alpha=1) +
labs(title = "Iris Sepal Length")+
labs(x="Sepal Length", y="Count")
iris.list<-by(data = iris, INDICES = iris$Species, simplify = TRUE,FUN = function(x)
{iris.hp %+% x + ggtitle(unique(x$Species))})
#Generate list of data to create summary statistics table
sum.str<-aggregate(Sepal.Length~Species,iris,summary)
spec<-sum.str[,1]
spec.stats<-sum.str[,2]
sum.data<-data.frame(spec,spec.stats)
sum.table<-tableGrob(sum.data)
colnames(sum.data) <-c("species","sep.len.min","sep.len.1stQ","sep.len.med",
"sep.len.mean","sep. len.3rdQ","sep.len.max")
table.list<-by(data = sum.data, INDICES = sum.data$"species", simplify = TRUE,
FUN = function(x) {tableGrob(x)})
#Combined histogram and summary table across multiple plots
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list,table.list))),
nrow=2, ncol=1, top = quote(paste(iris$labels$Species,'\nPage', g, 'of',pages)))
#bypass the class check per #baptiste
ggsave <- ggplot2::ggsave; body(ggsave) <- body(ggplot2::ggsave)[-2]
#
for(i in 1:3){
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list[i],table.list[i]))),
nrow=2, ncol=1,heights=c(1.65,.35),
top = quote(paste(iris$labels$Species,'\nPage', g, 'of',pages)))
prefix<-unique(iris$Species)
prefix<-prefix[i]
filename<-paste(prefix,".svg",sep="")
ggsave(filename,multi.plots)
#dev.off()
}
Edit removed theme tt3 that #rawr referenced. It was accidentally left in example code. It was not causing the problem, just in case anyone was curious.
Edit: Removing previous answer regarding it working under 32bit install and not x64 install because that was not the problem. Still unsure what was causing the issue, but it is working now. Leaving the info about grid.export as it may be a useful alternative for someone else.
Below is the loop for saving the .svg's using grid.export(), although I was having some text formatting issues with this (different dataset).
for(i in 1:3){
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list[i],table.list[i]))),
nrow=2, ncol=1,heights=c(1.65,.35), top =quote(paste(iris$labels$Species,'\nPage', g,
'of',pages)))
prefix<-unique(iris$Species)
prefix<-prefix[i]
filename<-paste(prefix,".svg",sep="")
grid.draw(multi.plots)
grid.export(filename)
grid.newpage()
}
EDIT: As for using arrangeGrob per #baptiste's comment. Below is the updated code. I was incorrectly using the single brackets [] for the returned by list, so I switched to the correct double brackets [[]] and used grid.draw to on the ggsave call.
for(i in 1:3){
prefix<-unique(iris$Species)
prefix<-prefix[i]
multi.plots<-grid.arrange(arrangeGrob(iris.list[[i]],table.list[[i]],
nrow=2,ncol=1,top = quote(paste(iris$labels$Species))))
filename<-paste(prefix,".svg",sep="")
ggsave(filename,grid.draw(multi.plots))
}
I would like to plot a simple graphic. I have a dat set with n rowns and k columns, in which each row has a a sequence of 0 and 1. I would like to plot exactly this sequence for all rows.
Actually I want to reproduce the figure 24.1, p. 516, of Gelman and Hill's book (Data aAnalysis Using Regression and Multilevel/Hierarchical Models). I suspect that he made the graphic in Latex, but it seems quite ridiculous that I'm not able to repplicate this simple graphic in R. The figue is something like this. As you can see from the link, the "ones" are replaced by "S" and "zeros" by ".". It's a simple graphic, but it shows each individual response by time.
I would go with a formatted text output using sprintf. Much cleaner and simpler. If you still want a plot, you could go with the following:
Given matrix tbl containing your data:
tbl <- matrix(data=rep(0:1,25), nrow=5)
You can generate a plot as:
plot(1, 1, xlim=c(1,dim(tbl)[2]+.5), ylim=c(0.5,dim(tbl)[1]), type="n")
lapply(1:dim(tbl)[1], function(x) {
text(x=c(1:dim(tbl)[2]), y=rep(x,dim(tbl)[2]), labels=tbl[x,])
})
Using this as a base you can play around with the text and plot args to stylize the plot the way you wish.
Here are two possible solutions, based on fake data generated with this helper function:
generate.data <- function(rate=.3, dim=c(25,25)) {
tmp <- rep(".", prod(dim))
tmp[sample(1:prod(dim), ceiling(prod(dim)*rate))] <- "S"
m <- matrix(tmp, nr=dim[1], nc=dim[2])
return(m)
}
Text-based output
x <- generate.data()
rownames(x) <- colnames(x) <- 1:25
capture.output(as.table(x), file="res.txt")
The file res.txt include a pretty-printed version of the console output; you can convert it to pdf using any txt to pdf converter (I use the one from PDFlib). Here is a screenshot of the text file:
Image-based output
First, here is the plotting function I used:
make.table <- function(x, labels=NULL) {
# x = matrix
# labels = list of labels for x and y
coord.xy <- expand.grid(x=1:nrow(x), y=1:ncol(x))
opar <- par(mar=rep(1,4), las=1)
plot.new()
plot.window(xlim=c(0, ncol(x)), ylim=c(0, nrow(x)))
text(coord.xy$x, coord.xy$y, c(x), adj=c(0,1))
if (!is.null(labels)) {
mtext(labels[[1]], side=3, line=-1, at=seq(1, ncol(x)), cex=.8)
mtext(labels[[2]], side=2, line=-1, at=seq(1, nrow(x)), cex=.8, padj=1)
}
par(opar)
}
Then I call it as
make.table(x, list(1:25, 1:25))
and here is the result (save it as png, pdf, jpg, or whatever).
As far as I can see, this is a text table. I am wondering why you want to make it a graph? Anyway, quick solutions are (either way)
make the text table (by programming or typing) and make its screenshot and embed the image into the plot.
make a blank plot and put the text on the plot by programming R with "text" function. For more info on "text", refer to http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_adtxt.html