Hi all,

I have written a simple R script to help me analyze a large data set.   
I would like to have the script pause to allow the user to input a  
character string that is subsequently used as a filename when saving  
tables.  I have tried to use the "readline" command - this seems to  
work fine when entering commands one by one, but when I copy and paste  
the entire script into R, it does not pause for input and just charges  
ahead writes the files.  Any help is appreciated, I've copied and  
pasted the script below.  Any help is appreciated - I am really new to  
R so if you can be as detailed as possible in your responses it would  
be greatly appreciated.

Thanks,

JT

R version: R 2.11.1 GUI 1.34
OS: OS 10.5.8

Here's the script:

#readfiles, "a" is nuclear measurements, "b" is cytoplasmic measurements
a <- read.table(file.choose(), header=TRUE, sep=",")
b <- read.table(file.choose(), header=TRUE, sep=",")

#make a new data frame named "new" with important columns
new <- data.frame(a$ImageNumber, a$AreaShape_Area, a 
$Intensity_IntegratedIntensity_OrigRFP, a 
$Intensity_IntegratedIntensity_OrigGFP, b 
$Intensity_MeanIntensity_OrigGFP)

#make three new columns, "EstCytoIntensity" estimates Cytoplasmic  
intensity based on the mean measured intensity and an estimate of the  
nuclear volume to the cytoplasmic volume, "TotalIntensity" is the sum  
of the integrated nuclear intensity and estimated cytoplasmic  
intensity, "NucToCytoRatio" is the ratio of nuclear intensity divided  
by cytoplasmic intensity
new$EstCytoIntensity <- b$Intensity_MeanIntensity_OrigGFP * (a 
$AreaShape_Area/0.3)
new$TotalIntensity <- new$a.Intensity_IntegratedIntensity_OrigGFP + new 
$EstCytoIntensity
new$NucToCytoRatio <- new$a.Intensity_IntegratedIntensity_OrigGFP / new 
$TotalIntensity

#creates a table that determines the means for the measurements of all  
objects within an image
library(plyr)
newmean <- ddply(new, c("a.ImageNumber"), summarize,  
NuclearMean=mean(a.Intensity_IntegratedIntensity_OrigGFP, trim=0.01),  
CytoMean=mean(EstCytoIntensity, trim=0.01),  
IntensityMean=mean(TotalIntensity, trim=0.01),  
RatioMean=mean(NucToCytoRatio, trim=0.01))

# input file name
name <- readline(prompt="give filename ")

#writes tables based on name given, both 'raw' containing all  
information and 'mean' containing the image means

write.table(new, file=paste(name,"raw.csv", sep=""), row.names=FALSE,  
sep=",")
write.table (newmean, file=paste(name, "mean.csv", sep=""),  
row.names=FALSE, sep=",")

#end





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