[R] Plotting patient drug timelines using ggplot2 (or some other means) -- Help!!!
Paul Miller
pjmiller_57 at yahoo.com
Thu Mar 22 22:48:12 CET 2012
Hi Michael,
Want to reverse the ordering of drugs on the y-axis. So tried scale_y_reverse() instead of scale_x_reverse(). Sure enough, the command exits. Unfortunately, it is "unsuitable for factors". I tried converting "drug" to character but this didn't work. Suspect scale_x_reverse() only works for something numeric which I don't think is helpful in my case. So changing "drug" to an ordered factor may make sense. I found some stuff online suggesting this approach.
The suggestion for setting the size of the image device directly was very helpful.
My code now looks like:
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
TestData$drug <- factor(TestData$drug, levels = c("Drug D", "Drug C", "Drug B", "Drug A"))
png(filename="plot21.png", width=600, height=300)
ggplot(TestData, aes(value, drug)) + geom_line(size = 6) + xlab("") + ylab("") + theme_bw() +
opts(title = "Pattern = Begin (A), Begin (B), End (B), End (A) \n (profile_key = 2, line = 1)") +
opts(axis.text.x = theme_blank() )
dev.off()
This produces a perfectly sized image. I imported the image created into Word and it looks like I would get 3 images per page.
As far as the text at the top of the graphs goes, I have 4 patient x line combinations in my data (at least before I filter to get a single patient by line combination). So the text at the top of each graph (without any filtering) would be as follows:
Pattern = Begin (A), Begin (B), End (B), End (A)
(profile_key = 1, line = 1)
Pattern = Begin (A, B, C), End (A, B), End (C)
(profile_key = 1, line = 2)
Pattern = Begin (A, B), End (A, B), Begin (C), End (C), Begin (D), End (D)
(profile_key = 2, line = 1)
Pattern = Begin (A, B), End (A, B)
(profile_key = 2, line = 2)
As far as I know, there's nothing like this online. I hope this makes it clear though.
The last part would be looping. I think I could figure out how to do this using a for loop or some other means if I can get one of the graphs set up correctly. The graphs themselves might be called something like plot11, plot12, plot21, and plot22.
Thanks,
Paul
--- On Thu, 3/22/12, R. Michael Weylandt <michael.weylandt at gmail.com> wrote:
> From: R. Michael Weylandt <michael.weylandt at gmail.com>
> Subject: Re: [R] Plotting patient drug timelines using ggplot2 (or some other means) -- Help!!!
> To: "Paul Miller" <pjmiller_57 at yahoo.com>
> Cc: r-help at r-project.org
> Received: Thursday, March 22, 2012, 4:11 PM
> On Thu, Mar 22, 2012 at 4:47 PM, Paul
> Miller <pjmiller_57 at yahoo.com>
> wrote:
> > Hi Michael,
> >
> > Made some progress but not there yet.
> >
> > Got point #1 by creating an ordered factor. There
> doesn't appear to be a command called Scale_x_flip().
> >
>
> Sorry, my mistake: I meant scale_x_reverse() ...
>
> > Still not sure how to decrease vertical space between
> the line segments for each drug. Thought this would be
> necessary in order to get a fair number of graphs onto a
> page in Word or in a pdf (say 4-5). I had imagined creating
> graphs that would be wider than they are tall in order to
> accomplish this.
>
> You can set the size of the image device directly, e.g.,
> png(....,
> width = 400, height = 200) and then make your plots one per
> image,
> closing the device with dev.off() when you're done. I think
> getting
> multiple plots per page (without facetting) won't be super
> easy and
> requires a few tricks with grid tools; someone might know
> better.
>
> I know pdf() supports multiple pages if you plot multiple
> graphs and
> don't close the device between, but I'm not sure that's
> doable with
> the other ones.
>
> >
> > Removed numbering from the x-axis using
> "opts(axis.text.x = theme_blank()". This is slightly
> different from the "opts(axis.ticks.x = theme_blank())" that
> you suggested. Having axis.ticks.x made it a lot easier to
> figure out I needed axis.text.x though.
> >
> > Got the text for pattern at the top (point #4).
> >
> > Still struggling with the text for patient and line
> (point #5). Managed to at least add some text manually to
> show what the text would look like for one of the graphs.
>
> I'm not sure what you are looking for here -- is there an
> image online
> you can point me too?
>
> >
> > Not sure how to get a separate graph for each patient x
> line combination. Discovered facets earlier today. Think
> this will just give me one giant graph though that contains
> graph for each patient x line combination.
> > This isn't so bad but it's not clear how one could
> print it and have the graphs break properly across pages.
> >
>
> As described above, you probably want to make multiple files
> by
> looping over your data and selecting subsets. I know Bert
> pointed you
> to xyplot in lattice graphics -- if you get that working, I
> believe it
> has some natural support for multi-page graphics but I don't
> know the
> package so well.
>
> > If you can provide any additional help, that's great.
> If not that's OK too. As I said earlier, there's a big time
> crunch around this. If I can't figure it out today, then
> we'll just move forward without it. Then I can figure out
> how to do it later for my own edification and at my own
> leisure. Chances are that will be a lot more fun than trying
> to learn under intense time pressure.
> >
> > 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
> >
> > TestData$drug <- factor(TestData$drug, levels =
> c("Drug D", "Drug C", "Drug B", "Drug A"))
> >
> > ggplot(TestData, aes(value, drug)) + geom_line(size =
> 6) + xlab("") + ylab("") + theme_bw() +
> > opts(title = "Pattern = Begin
> (A), Begin (B), End (B), End (A) \n (profile_key = 2, line =
> 1)") +
> > opts(axis.text.x =
> theme_blank() )
> >
> >
> >
> > --- On Thu, 3/22/12, R. Michael Weylandt <michael.weylandt at gmail.com>
> wrote:
> >
> >> From: R. Michael Weylandt <michael.weylandt at gmail.com>
> >> Subject: Re: [R] Plotting patient drug timelines
> using ggplot2 (or some other means) -- Help!!!
> >> To: "Paul Miller" <pjmiller_57 at yahoo.com>
> >> Cc: r-help at r-project.org
> >> Received: Thursday, March 22, 2012, 12:55 PM
> >> Inline:
> >>
> >> On Thu, Mar 22, 2012 at 1:41 PM, 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.
> >>
> >> Scale_x_flip()
> >>
> >> >
> >> > 2. Decrease the vertical space between the
> line
> >> segments for each drug so they are fairly close to
> one
> >> another.
> >>
> >> Why? This will happen automatically if needed....
> >>
> >> >
> >> > 3. Remove the numbering from the x-axis.
> >>
> >> opts(axis.ticks.x = theme_blank())
> >>
> >> >
> >> > 4. Put the text for pattern above the graph
> (e.g.,
> >> "Begin (A), Begin (B), End (B), End (A)"), either
> centered
> >> or left aligned.
> >>
> >>
> >> opts(title = "Begin (A), Begin (B), End (B), End
> (A)")
> >>
> >> >
> >> > 5. Put the patient and line information below
> the text
> >> for pattern (e.g., "profile_key = 1, line = 1")
> >>
> >> example(geom_text)
> >> or
> >> https://learnr.wordpress.com/2010/01/03/directlabels-adding-direct-labels-to-ggplot2-and-lattice-plots/
> >>
> >> >
> >> > 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.
> >>
> >> Google Sweave or (possibly easier) knitr
> >>
> >> >
> >> > 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()
> >>
> >> It would be easier if you could use dput() but this
> was
> >> helpfully reproducible.
> >>
> >> Hope this gets you started,
> >>
> >> Michael
> >>
> >> > 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.
> >>
>
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