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

[Bert Gunter]

The message apparently sent itself  before I was ready . :-(

Here's the full version. I hope I have interpreted your intent
correctly. Ignore if I have not.


 A general approach to this sort of thing is to get your data in "long"
 format, like this

 patientID   time   value
  A          1          .029
  A          2         .053
.
.
.
  B       1            1.25
.
.
.

The ID's do not need to appear in order or together. The times need
not be in order.

Once the data are in this form, xyplot() in lattice can do it via:

xyplot( value ~ time , group = patientID, type = "c("l","p"), auto.key=TRUE )

?xyplot for additional info.


-- Bert









>
> On Thu, Mar 22, 2012 at 10:41 AM, Paul Miller <pjmiller_57 at yahoo.com> wrote:
>> Hello All,
>>
>> Want very much to learn how to plot patient drug timelines. Trouble is I need to figure out how to do this today. So not much time for me to struggle with it. Hoping someone can just help me out a bit.
>>
>> Below are some sample data and code that produces what I think is the beginning of a very nice graph.
>>
>> Need to alter the code to:
>>
>> 1. Get the lines for the drugs to appear on the y-axis in the order that they appear in the data.
>>
>> 2. Decrease the vertical space between the line segments for each drug so they are fairly close to one another.
>>
>> 3. Remove the numbering from the x-axis.
>>
>> 4. Put the text for pattern above the graph (e.g., "Begin (A), Begin (B), End (B), End (A)"), either centered or left aligned.
>>
>> 5. Put the patient and line information below the text for pattern (e.g., "profile_key = 1, line = 1")
>>
>> 6. Output a separate graph for each patient and line of treatent.
>>
>> Ultimately, I want to combine all the graphs into a single Word document. Or perhaps better yet, to create a pdf using LaTeX.
>>
>> I'm going to continue to try and fugure this out as best I can. Any help with it will be greatly appreciated though.
>>
>> 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$profile_key == 2 & TestData$line == 1,]
>> TestData
>>
>> require(reshape)
>> TestData <- melt(TestData, measure.vars = c("start_drug", "stop_drug"))
>> TestData
>>
>> ggplot(TestData, aes(value, drug)) + geom_line(size = 6) + xlab("") + ylab("") + theme_bw()
>> ggsave(file = "plot21.pdf")
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm



-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm