I am outputting plots as png based on grouping according to the dataframe vector called "chr". This generates lots of plots but I would like to have them all in one png. I am using the plot function in r rather than ggplot2.
My code so far:
for(jj in ind){
png(paste("/Users/sebastianzeki/Desktop/SequencingScripts/Plots/",jj,".png"))
indic = which(ret$chr == jj)
plot(ret$binRight[indic],ret$SummedZScore[indic],pch=19,xlab="Locus",ylab="Summed ZScore",type="h",lwd=20, space=0)
dev.off()
How can I get all the plots on one png (or pdf if thats easier)?
Suppose length(ind) = 10
png(paste("/Users/sebastianzeki/Desktop/SequencingScripts/Plots/",jj,".png"))
par(mfrow=c(5,2))
for(jj in ind){
indic = which(ret$chr == jj)
plot(ret$binRight[indic],ret$SummedZScore[indic],pch=19,xlab="Locus",ylab="Summed ZScore",type="h",lwd=20, space=0)
}
dev.off()
This can make one png file or if you want to make a pdf file
How to print R graphics to multiple pages of a PDF and multiple PDFs?
Look at the above thread for help.
A simple example :
png("temp.png", width = 600, height = 2000)
par(mfrow=c(8,3), mar = rep(0.5, 4), oma = rep(0.5, 4))
for (i in 1:24) {
hist(runif(20), main = NULL)
}
dev.off()
Related
I am trying to create a multipage pdf with multiple plots per page from a list of plots created using base R plot() function. I know this is easy if the plots are created using ggplot2, but the plots I have come from a package that uses base R plot(). I store the plots in a list and then want to create a pdf from the list of plots. The following section of code gives a working example of what I am after:
# This creates 1 file with multiple pages & each page having 4 plots
pdf(file = if(TRUE) "Rplot.pdf" else "Rplot%03d.pdf",
paper = "letter")
par(mfrow=c(nrow = 2, ncol = 2))
for (i in 1:6){
x=rnorm(5)
y=rnorm(5)
plot(x,y)
title(paste0("Plot ",i))
}
I am trying to obtain the same result when the plots are stored in a list, as in the following:
# Create plots and store in a list
listofplots <- list()
for (i in 1:6){
x=rnorm(5)
y=rnorm(5)
plot(x,y)
title(paste0("Plot ",i))
listofplots[[i]] <- recordPlot()
}
# Create pdf
pdf(file = "Rplot.pdf")
par(mfrow=c(nrow = 2, ncol = 2))
for(i in 1:6) {
print(listofplots[[i]])
}
dev.off()
The above code generates 1 file, with 1 plot per page, rather than multiple plots per page. Clearly I am missing something simple.
I would like to save multiple plots (with ggplot2) to a list during a large for-loop. And then subsequently display the images in a grid (with grid.arrange)
I have tried two solutions to this:
1 storing it in a list, like so:
pltlist[["qplot"]] <- qplot
however for some reason this does save the plot correctly.
So I resorted to a second strategy which is recordPlot()
This was able to save the plot correctly, but unable to
use it in a grid.
Reproducable Example:
require(ggplot2);require(grid);require(gridExtra)
df <- data.frame(x = rnorm(100),y = rnorm(100))
histoplot <- ggplot(df, aes(x=x)) + geom_histogram(aes(y=..density..),binwidth=.1,colour="black", fill="white")
qplot <- qplot(sample = df$y, stat="qq")
pltlist <- list()
pltlist[["qplot"]] <- qplot
pltlist[["histoplot"]] <- histoplot
grid.arrange(pltlist[["qplot"]],pltlist[["histoplot"]], ncol=2)
above code works but produces the wrong graph
in my actual code
Then I tried recordPlot()
print(histoplot)
c1 <- recordPlot()
print(qplot)
c2 <- recordPlot()
I am able to display all the plots individually
but grid.arrange produces an error:
grid.arrange(replayPlot(c1),replayPlot(c2), ncol=2) # = Error
Error in gList(list(wrapvp = list(x = 0.5, y = 0.5, width = 1, height = 1, :
only 'grobs' allowed in "gList"
In this thread Saving grid.arrange() plot to file
They dicuss a solution which utilizes arrangeGrob() instead
arrangeGrob(c1, c1, ncol=2) # Error
Error in vapply(x$grobs, as.character, character(1)) :
values must be length 1,
but FUN(X[[1]]) result is length 3
I am forced to use the recordPlot() instead of saving to a list since this does not produce the same graph when saved as when it is plotted immediately, which I unfortunately cannot replicate, sorry.
In my actual code I am doing a large for-loop, looping through several variables, making a correlation with each and making scatterplots, where I name the scatterplots dependent on their significans level. I then want to re-display the plots that were significant in a grid, in a dynamic knitr report.
I am aware that I could just re-plot the plots that were significant after the for-loop instead of saving them, (I can't save as png while doing knitr either). However I would like to find a way to dynammically save the plots as R-objects and then replot them in a grid afterwards.
Thanks for Reading
"R version 3.2.1"
Windows 7 64bit - RStudio - Version 0.99.652
attached base packages:
[1] grid grDevices datasets utils graphics stats methods base
other attached packages:
[1] gridExtra_2.0.0 ggplot2_1.0.1
I can think of two solutions.
1. If your goal is to just save the list of plots as R objects, I recommend:
saveRDS(object = pltlist, file = "file_path")
This way when you wish to reload in these graphs, you can just use readRDS(). You can then put them in cowplot or gridarrange. This command works for all lists and R Objects.
One caveat to this approach is if settings/labeling for ggplot2 is dependent upon things in the environment (not the data, but stuff like settings for point size, shape, or coloring) instead of the ggplot2 function used to make the graph), your graphs won't work until you restore your dependencies. One reason to save some dependencies is to modularize your scripts to make the graphs.
Another caveat is performance: From my experience, I found it is actually faster to read in the data and remake individual graphs than load in an RDS file of all the graphs when you have a large number of graphs (100+ graphs).
2. If your goal is to save an 'image' or 'picture' of each graph (single and/or multiplot as .png, .jpeg, etc.), and later adjust things in a grid manually outside of R such as powerpoint or photoshop, I recommend:
filenames <- c("Filename_1", "Filename_2") #actual file names you want...
lapply(seq_along(pltlist), function(i) {
ggsave(filename = filenames[i], plot = pltlist[[i]], ...) #use your settings here
})
Settings I like for single plots:
lapply(seq_along(pltlist), function(i) ggsave(
plot = pltlist[[i]],
filename = paste0("plot_", i, "_", ".tiff"), #you can even paste in pltlist[[i]]$labels$title
device = "tiff", width=180, height=180, units="mm", dpi=300, compression = "lzw", #compression for tiff
path = paste0("../Blabla") #must be an existing directory.
))
You may want to do the manual approach if you're really OCD about the grid arrangement and you don't have too many of them to make for publications. Otherwise, when you do grid.arrange you'll want to do all the specifications there (adjusting font, increasing axis label size, custom colors, etc.), then adjust the width and height accordingly.
Reviving this post to add multiplot here, as it fits exactly.
require(ggplot2)
mydd <- setNames( data.frame( matrix( rep(c("x","y","z"), each=10) ),
c(rnorm(10), rnorm(10), rnorm(10)) ), c("points", "data") )
# points data
# 1 x 0.733013658
# 2 x 0.218838717
# 3 x -0.008303382
# 4 x 2.225820069
# ...
p1 <- ggplot( mydd[mydd$point == "x",] ) + geom_line( aes( 1:10, data, col=points ) )
p2 <- ggplot( mydd[mydd$point == "y",] ) + geom_line( aes( 1:10, data, col=points ) )
p3 <- ggplot( mydd[mydd$point == "z",] ) + geom_line( aes( 1:10, data, col=points ) )
multiplot(p1,p2,p3, cols=1)
multiplot:
multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
library(grid)
# Make a list from the ... arguments and plotlist
plots <- c(list(...), plotlist)
numPlots = length(plots)
# If layout is NULL, then use 'cols' to determine layout
if (is.null(layout)) {
# Make the panel
# ncol: Number of columns of plots
# nrow: Number of rows needed, calculated from # of cols
layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
ncol = cols, nrow = ceiling(numPlots/cols))
}
if (numPlots==1) {
print(plots[[1]])
} else {
# Set up the page
grid.newpage()
pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
# Make each plot, in the correct location
for (i in 1:numPlots) {
# Get the i,j matrix positions of the regions that contain this subplot
matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
layout.pos.col = matchidx$col))
}
}
}
Result:
Here is the question where I have a number of plots and I want to revise them one by one visually at once pace.
xm <- matrix(runif(20000), ncol = 1000)
for (i in 1:ncol(xm)){
hist(xm[,i], col = i)
}
This loop will make the plots so fast that I will have slit second to look (or not at all) in graphical device.
There can be several way around:
(1) look plots one by one - press return key to see next plot
We can create a breaks and user can use return key to see next plot.
xm <- matrix(runif(20000), ncol = 1000)
for (i in 1:ncol(xm)){
hist(xm[,i], col = i, main = paste(i))
grDevices::devAskNewPage(ask = TRUE)
}
Note that default behavior in R is grDevices::devAskNewPage(ask = FALSE).
(2) input plot number you want see from keyboard
You select which variable you want to plot, this way you can avoid chronological visualization of the plots, or else you can input the plot number(s) you want, in the order you want and click stop when you are done.
for (i in 1:ncol(xm)){
i <- scan(nmax=1)
hist(xm[,i], col = i, main = paste(i))
}
(3) all plots in new windows
If you would like to make a new plot each time, you can use:
for (i in 1:10){
hist(xm[,i], col = i, main = paste(i))
dev.new()
}
(4) multiple plot in single window
If you like to plot multiple plots in a single plot:
par(mfrow = c(5,2))
for (i in 1:10){
hist(xm[,i], col = i, main = paste(i))
}
(5) Pdf file with multiple plots in separate page
Another way to save the files as PDF or other format:
The following will create output PDF will all figures in different page and then can scrolled down up.
pdf("outtrtt.pdf",width=7,height=5)
for (i in 1:ncol(xm)){
hist(xm[,i], col = i, main = paste(i))
}
dev.off()
(6) separate pdf files per plot
Or if you want to create output as single PDF file per plot or other image file types this may do so. Please note that this may be different in mac and windows.
for (i in 1:ncol(xm)){
pdf(paste("var", i, ".pdf", sep = ""),width=7,height=5)
hist(xm[,i], col = i, main = paste(i))
dev.off()
}
(7) separate image files
You can save as jpeg or other format of your choice
for (i in 1:ncol(xm)){
jpeg(paste("var", i, ".jpeg", sep = ""),width=700,height=500)
hist(xm[,i], col = i, main = paste(i))
dev.off()
}
Other answers are welcome.
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.
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