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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