I am struggling to figure out how to plot two transform() (dlookr library) plots together nicely in R Markdown. The following code results in the output from the picture included with this post. I want the last plot (2x2) and am wondering why the other two are populating as well. How can I only print the last one in Markdown?
# payment transformation
payment_log <- transform(my_data$payment, method = "log")
# income transformation
income_log <- transform(my_data$income, method = "log")
grid.arrange(
plot(payment_log,typographic=FALSE), # visual of transformation
plot(income_log,typographic=FALSE), # visual of transformation
ncol=1)
The first two plots can be avoided by wrapping each plot in a function call inside as.grob, and then passing these variables to grid.arrange.
library(dlookr)
library(ggplotify)
my_data=data.frame(payment=c(1,2,2,3,3,3,4,4,4,4,5,5,5,5,5,6,6,6,6,6,6,7,7,7,7,7,7,7,8,8,8,8,8,8,8,8,9,9,9,9,9,9,9,9,9),
income=c(1,2,2,3,3,3,4,4,4,4,5,5,5,5,5,6,6,6,6,6,6,7,7,7,7,7,7,7,8,8,8,8,8,8,8,8,9,9,9,9,9,9,9,9,9))
payment_log=transform(my_data$payment, method="log")
income_log=transform(my_data$income, method="log")
x=as.grob(function() plot(payment_log))
y=as.grob(function() plot(income_log))
grid.arrange(grobs=list(x,y), ncol=1)
Related
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 having problems using ggplot with Rmarkdown.
I have a code that is supposed to return a ggplot graph.When I execute the code in a R session it works but the same code returns an empty plot when using R markdown.This is the code I am using in the R session
m<-ggplot(data=t,aes_string(x=v,y =t$cnt_pct))
m+geom_bar(stat = "identity",fill="#FF0000",color='black')+geom_text(aes(label = cnt_pct),vjust=-0.2)+ggtitle(paste(v,paste("graph")))+theme(plot.title = element_text(hjust = 0.5))+ylab("percent")+geom_line(aes_string(x=v,y =t$keshel_pct),group=1,size=2)
This is the code I am using in the Rmarkdown
m<-ggplot(data=t,aes_string(x=v,y =t$cnt_pct))
m+geom_bar(stat = "identity",fill="#FF0000",color='black')+geom_text(aes(label = cnt_pct),vjust=-0.2)+ggtitle(paste(v,paste("graph")))+theme(plot.title = element_text(hjust = 0.5))+ylab("percent")+geom_line(aes_string(x=v,y =t$keshel_pct),group=1,size=2)
plot(m)
The only diffrence between the two is that with the Rmarkwond a plot(m) line is added.
For some reason the plot command makes the graph empty, when I remove it and run the Rmarkdown no graphs are returned.
This is the graph empty
This is the graph working in a session of R
Anybody has any idea what is my mistake?
Any help will be appriciated
You have a few issues here:
1) your plot syntax has issues. aes_string takes strings referring to column names, but you're passing a variable v for x and direct column data t$cnt_pnt for y. Check some ggplot examples to get the syntax right.
2) The plot(m) statement shouldn't work for two reasons: first, you print ggplot objects, not plot them. Second, you are not assigning the m + geom_bar(...) statement to anything, so even if your plot statement did work, you'd get the plot without the geom_bar(...) stuff. Try e.g. y = m+ geom_bar(...); print(y) instead.
I was experimenting with the waffle package in r, and was trying to use a for loop to make multiple plots at once but was not able to get my code to work. I have a dataset with values for each year of renewables,and since it is over 40 years of data, was looking for a simple way to plot these with a for loop rather than manyally year by year. What am I doing wrong?
I have it from 1:16 as an experiment to see if it would work, although in reality I would do it for all the years in my dataset.
for(i in 1:16){
renperc<-islren$Value[i]
parts <- c(`Renewable`=(renperc), `Non-Renewable`=100-renperc)
waffle(parts, rows=10, size=1, colors=c("#00CC00", "#A9A9A9"),
title="Iceland Primary Energy Supply",
xlab=islren$TIME)
}
If I get your question correctly you want to plot all the 16 iterations in a same panel? You can parametrise your plot window to be divided into 16 smaller plots using par(mfrow = c(4,4)) (creating a 4 by 4 matrix and plotting into each cells recursively).
## Setting the graphical parameters
par(mfrow = c(4,4))
## Running the loop normally
for(i in 1:16){
renperc<-islren$Value[i]
parts <- c(`Renewable`=(renperc), `Non-Renewable`=100-renperc)
waffle(parts, rows=10, size=1, colors=c("#00CC00", "#A9A9A9"),
title="Iceland Primary Energy Supply",
xlab=islren$TIME)
}
If you need more plots (e.g. 40) you can increase the numbers in the graphical parameters (e.g. par(mfrow = c(6,7))) but that will create really tiny plots. One solution is to do it in multiple loops (for(i in 1:16); for(i in 17:32); etc.)
UPDATE: The code simply wasn't plotting anything when i tried putting in anything above one value (ex. 1:16) or a letter, both in terms of separate plots or many in one plot window (which I think perhaps waffle does not support in the same way as regular plots). In the end, I managed by making it into a function, although I'm still not sure why my original method wouldn't work if this did. See the code that worked below. I also tweaked it a bit, adding ggsave for example.
#function
waffling <- function(x){
renperc<-islren$Value[x]
parts <- c(`Renewable`=(renperc), `Non-Renewable`=100-renperc)
waffle(parts, rows=10, size=1, colors=c("#00CC00", "#A9A9A9"), title="",
xlab=islren$TIME[x])
ggsave(file=paste0("plot_", x,".png"))}
for(i in 1:57){
waffling(i)
}
I have some 16 plots. I want to plot all of these in grid manner with ggplot2. But, whenever I plot, I get a grid with all the plots same, i.e, last plot saved in a list gets plotted at all the 16 places of grid. To replicate the same issue, here I am providing a simple example with two files. Although data are entirely different, but plots drawn are similar.
library(ggplot2)
library(grid)
library(gridExtra)
library(scales)
set.seed(1006)
date1<- as.POSIXct(seq(from=1443709107,by=3600,to=1446214707),origin="1970-01-01")
power <- rnorm(length(date1),100,5)#with normal distribution
write.csv(data.frame(date1,power),"file1.csv",row.names = FALSE,quote = FALSE)
# Now another dataset with uniform distribution
write.csv(data.frame(date1,power=runif(length(date1))),"file2.csv",row.names = FALSE,quote = FALSE)
path=getwd()
files=list.files(path,pattern="*.csv")
plist<-list()# for saving intermediate ggplots
for(i in 1:length(files))
{
dframe<-read.csv(paste(path,"/",files[i],sep = ""),head=TRUE,sep=",")
dframe$date1= as.POSIXct(dframe$date1)
plist[[i]]<- ggplot(dframe)+aes(dframe$date1,dframe$power)+geom_line()
}
grid.arrange(plist[[1]],plist[[2]],ncol = 1,nrow=2)
You need to remove the dframe from your call to aes. You should do that anyway because you have provided a data-argument. In this case it's even more important because while you save the ggplot-object, things don't get evaluated until the call to plot/grid.arrange. When you do that, it looks at the current value of dframe, which is the last dataset in your iteration.
You need to plot with:
ggplot(dframe)+aes(date1,power)+geom_line()
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()