You didn't do what I said.....
Once you make the list of data.frame()s "TempData", each single
element is a data.frame and that is what you need to pass to ggplot --
in the loop construct I set up, the individual data frame is called
temp so you need to have ggplot(temp).
As I said before,
## Do all your stuff -- just change "TestData" to "temp" so you are
using the right data.frame
I'll be a little more direct this time:
for(temp in TempData){
png(filename = paste("plot", unique(temp$key_line), ".png", sep = ""),
width=600, height=300)
p <- ggplot(temp, aes(value, drug)) + geom_line(size = 6) +
xlab("Time") + ylab("") + theme_bw() + opts(title = paste("Pattern =
", unique(temp$pattern), " \n (profile_key = ",
unique(temp$profile_key), ", line = ", unique(temp$line), ") \n", sep
= "")) + opts(axis.text.x = theme_blank())
print(p)
dev.off()
}
Michael
On Fri, Mar 23, 2012 at 10:22 AM, Paul Miller <pjmiller...@yahoo.com> wrote:
> Hi Michael and Petr,
>
> You both seem to have hit on the idea of splitting the TestData in order to
> do by group processing. Trouble is that ggplot2 doesn't seem to like lists
> very much.
>
> When I run the code:
>
> TempData <- split(TestData, TestData$key_line)
> TempData
>
> for(temp in TempData){
>
> png(filename = paste("plot", unique(TempData$key_line), ".png", sep = ""),
> width=600, height=300)
>
> ggplot(TempData, aes(value, drug)) + geom_line(size = 6) + xlab("Time") +
> ylab("") + theme_bw() +
> opts(title = paste("Pattern = ", unique(TempData$pattern), "
> \n (profile_key = ", unique(TempData$profile_key), ", line = ",
> unique(TempData$line), ") \n", sep = "")) +
> opts(axis.text.x = theme_blank() )
> dev.off()
>
> }
>
> I get the error message:
>
> "Error: ggplot2 doesn't know how to deal with data of class list"
>
> Are there any other good ways of doing the looping? Sorry to trouble you with
> this. If I had more time, I'd just struggle with it for awhile and figure it
> out myself.
>
> I tried embedding my ggplot code into print() as Petr suggested. I didn't
> think it would help but wanted to try just in case. No dice -- ggplot just
> doesn't seem to like lists.
>
> Thanks,
>
> Paul
>
>
>
> --- On Fri, 3/23/12, R. Michael Weylandt <michael.weyla...@gmail.com> wrote:
>
>> From: R. Michael Weylandt <michael.weyla...@gmail.com>
>> Subject: Re: [R] Plotting patient drug timelines using ggplot2 (or some
>> other means) -- Help!!!
>> To: "Paul Miller" <pjmiller...@yahoo.com>
>> Cc: r-help@r-project.org
>> Received: Friday, March 23, 2012, 8:52 AM
>> Inline.
>>
>> On Fri, Mar 23, 2012 at 9:40 AM, Paul Miller <pjmiller...@yahoo.com>
>> wrote:
>> > Hi Michael,
>> >
>> > Added a little more to my code (see below). It now
>> automatically sets the name of the file. It also does a
>> better job of spacing the text for pattern and patient x
>> line at the top of the graph.
>> >
>> > I really like the way this looks now. I just need to
>> figure out how to loop through the data using my "key_line"
>> (patient x line) variable.
>> >
>> > One of the things I've noticed while learning R is that
>> things I think will be difficult often go surprisingly well.
>> It's the things that I think will be easy that I wind up
>> struggling with. Right now I'm struggling with figuring out
>> how to loop through the data to produce plot11, plot 12,
>> plot21, and plot22.
>> >
>> > Embarassing. But there it is.
>> >
>> > Can you show me how to do that? In the meantime, I keep
>> working on it and may figure it out on my own.
>> >
>> > Thanks,
>> >
>> > Paul
>> >
>> >
>> > connection <- textConnection("
>> > 1/1/Drug A/ Begin (A), Begin (B), End (B), End
>> (A)/0.0000/21.000
>> > 1/1/Drug B/ Begin (A), Begin (B), End (B), End
>> (A)/0.7143/18.000
>> > 1/2/Drug A/ Begin (A, B, C), End (A, B), End
>> (C)/0.0000/20.000
>> > 1/2/Drug B/ Begin (A, B, C), End (A, B), End
>> (C)/0.0000/20.000
>> > 1/2/Drug C/ Begin (A, B, C), End (A, B), End
>> (C)/0.0000/36.000
>> > 2/1/Drug A/ Begin (A, B), End (A, B), Begin (C), End
>> (C), Begin (D), End (D)/0.0000/7.429
>> > 2/1/Drug B/ Begin (A, B), End (A, B), Begin (C), End
>> (C), Begin (D), End (D)/ 0.0000/7.429
>> > 2/1/Drug C/ Begin (A, B), End (A, B), Begin (C), End
>> (C), Begin (D), End (D)/ 14.5714/21.857
>> > 2/1/Drug D/ Begin (A, B), End (A, B), Begin (C), End
>> (C), Begin (D), End (D)/ 25.4286/231.286
>> > 2/2/Drug A/ Begin (A, B), End (A, B)/0.0000/35.286
>> > 2/2/Drug B/ Begin (A, B), End (A, B)/0.0000/35.286
>> > ")
>> >
>> > TestData <- data.frame(scan(connection,
>> list(profile_key=0, line=0, drug="", pattern="",
>> start_drug=0, stop_drug=0), sep="/"))
>> > TestData <- TestData[TestData$profile_key == 1 &
>> TestData$line == 1,]
>> > TestData
>> >
>> > require(reshape)
>> > TestData <- melt(TestData, measure.vars =
>> c("start_drug", "stop_drug"))
>> > TestData$drug <- factor(TestData$drug, levels =
>> c("Drug D", "Drug C", "Drug B", "Drug A"))
>> > TestData$key_line <-
>> with(TestData,paste(profile_key, line, sep = ""))
>> > TestData
>>
>> Useful trick: if you use dput() you can send this all in a
>> much more
>> concise fashion:
>>
>> structure(list(profile_key = c(1, 1, 1, 1), line = c(1, 1,
>> 1,
>> 1), drug = structure(c(4L, 3L, 4L, 3L), .Label = c("Drug
>> D",
>> "Drug C", "Drug B", "Drug A"), class = "factor"), pattern =
>> structure(c(4L,
>> 4L, 4L, 4L), .Label = c(" Begin (A, B, C), End (A, B), End
>> (C)",
>> " Begin (A, B), End (A, B)", " Begin (A, B), End (A, B),
>> Begin (C),
>> End (C), Begin (D), End (D)",
>> " Begin (A), Begin (B), End (B), End (A)"), class =
>> "factor"),
>> variable = structure(c(1L, 1L, 2L, 2L), .Label
>> = c("start_drug",
>> "stop_drug"), class = "factor"), value = c(0,
>> 0.7143, 21,
>> 18), key_line = c("11", "11", "11", "11")),
>> .Names = c("profile_key",
>> "line", "drug", "pattern", "variable", "value", "key_line"),
>> row.names = c(NA,
>> -4L), class = "data.frame")
>>
>>
>> >
>> > require(ggplot2)
>> >
>> > png(filename = paste("plot", unique(TestData$key_line),
>> ".png", sep = ""), width=600, height=300)
>> >
>> > ggplot(TestData, aes(value, drug)) + geom_line(size =
>> 6) + xlab("Time") + ylab("") + theme_bw() +
>> > opts(title = paste("Pattern =
>> ", unique(TestData$pattern), " \n (profile_key = ",
>> unique(TestData$profile_key), ", line = ",
>> unique(TestData$line), ") \n", sep = "")) +
>> > opts(axis.text.x =
>> theme_blank() )
>> >
>> > dev.off()
>> >
>> >
>>
>> If you want to loop over the different values of "key_line",
>> I think
>> it's pretty easy:
>>
>> TempData <- split(TestData, TestData$keyline) # List of
>> data frames
>>
>> for(temp in TempData){ # Loop over the list
>>
>> ## Do all your stuff -- just change "TestData" to "temp" so
>> you are
>> using the right data.frame
>>
>>
>> }
>>
>> Hope this helps,
>>
>> Michael
>>
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