[R] Plotting patient drug timelines using ggplot2 (or some other means) -- Help!!!

[R. Michael Weylandt]

Inline.

On Fri, Mar 23, 2012 at 9:40 AM, Paul Miller <pjmiller_57 at 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