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))
}
Related
I am enjoying the patchwork package quite a bit and I am generally happy with even its default formatting.
However, I cannot figure out how to get a reasonable result when trying to display many plots. The output is unreadable (plots shrunk down and dominated by text) and the saved output is completely blank.
Input:
require(ggplot2)
require(patchwork)
plots <- list()
testfunction <- function(x) {
plot_placeholder <- ggplot(mtcars) +
geom_point(aes(mpg, disp)) +
ggtitle(paste("p", x, sep = ""))
plots[[length(plots) + 1]] <<- plot_placeholder
}
mapply(testfunction, c(1:66), SIMPLIFY = FALSE)
patchwork::wrap_plots(plots)
ggsave("test.pdf")
Output:
Is there a way within patchwork to make the page larger or wrap plots across multiple pages of a PDF? Or is there a different package that may help with this?
Update:
Maurits Evers pointed out that this is an issue with my arguments in ggsave(), not patchwork. With these changes the plots look much better in the .pdf output, but were still being truncated at the bottom of page 1. From this post, found the last bit of change needed to generate desired results
Input:
# ...
pdf()
patchwork::wrap_plots(plots)
ggsave("test.pdf", width = 20, height = 20)
dev.off()
Output:
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 have a working loop which generates and can save individual plots from each file saved in a directory.
I want to plot all of the returned plots in a single file as a 2x2 grid over multiple pages but cannot do this.
I have tried to save the plot objects in a list
pltList <- list()
pltList[]
for (f in 1:length(files)){
plot_object <- ggplot2(...) #make ggplot2 plot
print(plot_object)
pltList[[f]] <- plot_object #save ggplot2 plot in list
}
jpeg(filename.jpg)
par(mfrow=c(2,2)) #to generate 2x2 plot per page
print(pltList[[1]])
print(pltList[[2]])
...
print(pltList[[f]])
dev.off()
The problem is that the resulting saved .jpg file only contains the last plot and not a 2x2 grid of all plots over many pages which is what I want.
EDIT
My first problem is how to save each plot from the loop in the list - how can I view the saved objects from the list to make sure they have been saved correctly?
When I do print(pltList[1]), the resulting output is:
function (x, y, ...)
UseMethod("plot")
<bytecode: 0x0000000010f43b78>
<environment: namespace:graphics>
rather than the actual plot. It seems that the plots are not being saved in the list as expected. How can I correct for this?
Hopefully, once this is fixed, your plotting suggestions will work.
I did recently the same. I used grid.arrange().
library(ggplot2)
library(gridExtra)
library(grid)
p1<-ggplot()+geom_line(aes(x=1:10,y=1:10))
p2<-ggplot()+geom_line(aes(x=1:10,y=1:10))
p3<-ggplot()+geom_line(aes(x=1:10,y=1:10))
p4<-ggplot()+geom_line(aes(x=1:10,y=1:10))
grid.arrange(p1,p2,p3,p4, ncol=1, top=textGrob("Multiple Plots", gp=gpar(fontsize=12, font = 2)))
Assuming you need a PDF output where every page has multiple plots plotted as one, e.g.: if there are 12 plots then 4 plots per page.
Try this example:
library(ggplot2)
library(cowplot)
# list of 12 dummy plots, only title is changing.
pltList <- lapply(1:12, function(i){
ggplot(mtcars,aes(mpg,cyl)) +
geom_point() +
ggtitle(paste("Title",i))})
# outputs 3 jpeg files with 4 plots each.
for(i in seq(1,12,4))
ggsave(paste0("Temp",i,".jpeg"),
plot_grid(pltList[[i]],
pltList[[i+1]],
pltList[[i+2]],
pltList[[i+3]],nrow = 2))
# or we can output into 1 PDF with 3 pages using print
pdf("TempPDF.pdf")
for(i in seq(1,12,4))
print(plot_grid(pltList[[i]],
pltList[[i+1]],
pltList[[i+2]],
pltList[[i+3]],nrow = 2))
dev.off()
EDIT:
Another way using gridExtra, as suggested by #user20650:
library(gridExtra)
#output as PDF
pdf("multipage.pdf")
#use gridExtra to put plots together
marrangeGrob(pltList, nrow=2, ncol=2)
dev.off()
I have several subjects for which I need to generate a plot, as I have many subjects I'd like to have several plots in one page rather than one figure for subject.
Here it is what I have done so far:
Read txt file with subjects name
subjs <- scan ("ListSubjs.txt", what = "")
Create a list to hold plot objects
pltList <- list()
for(s in 1:length(subjs))
{
setwd(file.path("C:/Users/", subjs[[s]])) #load subj directory
ifile=paste("Co","data.txt",sep="",collapse=NULL) #Read subj file
dat = read.table(ifile)
dat <- unlist(dat, use.names = FALSE) #make dat usable for ggplot2
df <- data.frame(dat)
pltList[[s]]<- print(ggplot( df, aes(x=dat)) + #save each plot with unique name
geom_histogram(binwidth=.01, colour="cyan", fill="cyan") +
geom_vline(aes(xintercept=0), # Ignore NA values for mean
color="red", linetype="dashed", size=1)+
xlab(paste("Co_data", subjs[[s]] , sep=" ",collapse=NULL)))
}
At this point I can display the single plots for example by
print (pltList[1]) #will print first plot
print(pltList[2]) # will print second plot
I d like to have a solution by which several plots are displayed in the same page, I 've tried something along the lines of previous posts but I don't manage to make it work
for example:
for (p in seq(length(pltList))) {
do.call("grid.arrange", pltList[[p]])
}
gives me the following error
Error in arrangeGrob(..., as.table = as.table, clip = clip, main = main, :
input must be grobs!
I can use more basic graphing features, but I d like to achieve this by using ggplot. Many thanks for consideration
Matilde
Your error comes from indexing a list with [[:
consider
pl = list(qplot(1,1), qplot(2,2))
pl[[1]] returns the first plot, but do.call expects a list of arguments. You could do it with, do.call(grid.arrange, pl[1]) (no error), but that's probably not what you want (it arranges one plot on the page, there's little point in doing that). Presumably you wanted all plots,
grid.arrange(grobs = pl)
or, equivalently,
do.call(grid.arrange, pl)
If you want a selection of this list, use [,
grid.arrange(grobs = pl[1:2])
do.call(grid.arrange, pl[1:2])
Further parameters can be passed trivially with the first syntax; with do.call care must be taken to make sure the list is in the correct form,
grid.arrange(grobs = pl[1:2], ncol=3, top=textGrob("title"))
do.call(grid.arrange, c(pl[1:2], list(ncol=3, top=textGrob("title"))))
library(gridExtra) # for grid.arrange
library(grid)
grid.arrange(pltList[[1]], pltList[[2]], pltList[[3]], pltList[[4]], ncol = 2, main = "Whatever") # say you have 4 plots
OR,
do.call(grid.arrange,pltList)
I wish I had enough reputation to comment instead of answer, but anyway you can use the following solution to get it work.
I would do exactly what you did to get the pltList, then use the multiplot function from this recipe. Note that you will need to specify the number of columns. For example, if you want to plot all plots in the list into two columns, you can do this:
print(multiplot(plotlist=pltList, cols=2))
I have found that the beanplot is the best way to represent my data. I want to look at multiple beanplots together to visualize my data. Each of my plots contains 3 variables, so each one looks something like what would be generated by this code:
library(beanplot)
a <- rnorm(100)
b <- rnorm(100)
c <- rnorm(100)
beanplot(a, b ,c ,ylim = c(-4, 4), main = "Beanplot",
col = c("#CAB2D6", "#33A02C", "#B2DF8A"), border = "#CAB2D6")
(Would have just included an image but my reputation score is not high enough, sorry)
I have 421 of these that I want to put into one long PDF (EDIT: One plot per page is fine, this was just poor wording on my part). The approach I have taken was to first generate the beanplots in a for loop and store them in a list at each iteration. Then I will use the multiplot function (from the R Cookbook page on multiplot) to display all of my plots on one long column so I can begin my analysis.
The problem is that the beanplot function does not appear to be set up to assign plot objects as a variable. Example:
library(beanplot)
a <- rnorm(100)
b <- rnorm(100)
plot1 <- beanplot(a, b, ylim = c(-5,5), main = "Beanplot",
col = c("#CAB2D6", "#33A02C", "#B2DF8A"), border = "#CAB2D6")
plot1
If you then type plot1 into the R console, you will get back two of the plot parameters but not the plot itself. This means that when I store the plots in the list, I am unable to graph them with multiplot. It will simply return the plot parameters and a blank plot.
This behavior does not seem to be the case with qplot for example which will return a plot when you recall the stored plot. Example:
library(ggplot2)
a <- rnorm(100)
b <- rnorm(100)
plot2 <- qplot(a,b)
plot2
There is no equivalent to the beanplot that I know of in ggplot. Is there some sort of workaround I can use for this issue?
Thank you.
You can simply open a PDF device with pdf() and keep the default parameter onefile=TRUE. Then call all your beanplot()s, one after the other. They will all be in one PDF document, each one on a separate page. See here.