qplot and commandArgs problem

[scott smith]

Hi,

I'm trying to write a simple .R script to produce plots from a .csv file specified in the command line.

for example, the following will plot LSS vs RSS from the scott_dose.csv file:

scott.smith@cougar:/home/scott.smith {31} Rscript Rtest.R scott_dose.csv LSS RSS

and the .R script is:

library(ggplot2)
args <- commandArgs(TRUE)

data<-data.frame(read.csv(args[1]))
attach(data)

x <- args[1]
y <- args[2]
z <- args[3]

x
y
z


qplot(y,z)

ggsave("~/tmp/RTest.png")

browseURL("~/tmp/RTest.png")

which produces a graph output, but with no data plotted:

scott.smith@cougar:/home/scott.smith {31} Rscript Rtest.R scott_dose.csv LSS RSS
Loading required package: methods
[1] "scott_dose.csv"
[1] "LSS"
[1] "RSS"
Saving 7 x 7 in image

Basically my "y" and "z" variables from commandArgs aren't being picked up by qplot. I'm sure it is something very simple, but I'm a relative beginner to R.

thanks, Scott

[Ben Bond-Lamberty]

Probably change your script to

p <- qplot( y, z )
ggsave("~/tmp/RTest.png", plot=p)

qplot doesn't produce any output inside of a script without being
explicitly print'ed.

Ben

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[scott smith]

Hi Ben,

Thanks - but unfortunately no change....image attached for reference....exactly the same as my original script.

library(ggplot2)
args <- commandArgs(TRUE)

data<-data.frame(read.csv(args[1]))
attach(data)

x <- args[1]
y <- args[2]
z <- args[3]

x
y
z

p <- qplot(y,z)

ggsave("~/tmp/RTest.png",plot=p)

browseURL("~/tmp/RTest.png")



thanks,
Scott

[Brandon Hurr]

The picture looks fine to me... RSS on the y axis, LSS on the x axis... scatterplot. 

[scott smith]

oops, thats how the graph SHOULD look when I do a qplot(LSS,RSS)!!

attached is the empty graph...

Scott

[Brandon Hurr]

I wouldn't say that's empty. There is clearly at least one point located at z,y, which makes me think that it's an issue with ""'s. 

I think it is plotting text versus text instead of your values. I believe you need to use ggplot(data=data, aes_string(x=y, y=z))+geom_point()

[scott smith]

Fantastic Brandon thanks!

Works perfectly.

Was trying to be quick and test it out with qplot.......should have plunged straight into ggplot

thanks,
Scott