After opening a PDF device, simply make serial calls to the plots. Each new plot will create a new page in the PDF file.

Example (not working by copy&paste, just for illustration):

pdf(...)

plot(y~x)

boxplot(df)

hist(y)

dev.off()

will create a pdf with 3 pages and a scatterplot on page 1, a boxplot on page 2 and a histogram on page 3.

EDIT:

The parameter "onefile" should be set to FALSE, what is the default. If this is not changed to TRUE and if the file is not a pipe, multiple pages will be created. Please have a look at the help page (?pdf):

onefile: logical: if true (the default) allow multiple figures in one file. If false, generate a file with name containing the page number for each page. Defaults to TRUE, and forced to true if file is a pipe.

After opening a PDF device, simply make serial calls to the plots. Each new plot will create a new page in the PDF file.

Example (not working by copy&paste, just for illustration):

pdf(...)

plot(y~x)

boxplot(df)

hist(y)

dev.off()

will create a pdf with 3 pages and a scatterplot on page 1, a boxplot on page 2 and a histogram on page 3.

EDIT:

The parameter "onefile" should be set to FALSE, what is the default. If this is not changed to TRUE and if the file is not a pipe, multiple pages will be created. Please have a look at the help page (?pdf):

onefile: logical: if true (the default) allow multiple figures in one file. If false, generate a file with name containing the page number for each page. Defaults to TRUE, and forced to true if file is a pipe.

@Jochen Wilhelm :great thanks for your detailed answer. a question added, if I want to save pictures which are generated in one operation(eg MA plot for 56 cel files),how can I save these pictures with several pages

Nan, this is written in the help. Set the argument "onefile=FALSE". You can use "%d" in the filename to indicate a position wher the plot number is placed. Another way is to create and close separate plots in a loop, for example

for (i in 1:nFiles) {

pdf(file=paste0(filnames[i],".pdf",...)

plotMA(celdata[i],...)

dev.off()

}

Hi

I love to have all plots in same PDF file, would please show me how to do that code.

thanking you

pdf(...) # create the PDF device

for (i in 1:nFiles) plotMA(celdata[i],...) # make all the plots

dev.off() # close the devide.