R help - Mar 2012 - Adding text for written comments to bottom of graphs

Hello All,

Recently developed the code below for graphing patterns of chemotherapy
administration. As someone just starting to use R in their work, I managed to
figure out some parts of the code but needed help with others.

setwd("N:/Regimen Coding/0906/Plots Test")
getwd()

TestData <- structure(list(profile_key = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 
2, 3, 3, 3, 3, 3), line = c(1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 
1, 1, 1, 1, 1), instance = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 2), drug = structure(c(1L, 2L, 1L, 2L, 3L, 1L, 2L, 
3L, 4L, 1L, 2L, 2L, 1L, 3L, 4L, 3L), .Label = c("Drug A", "Drug
B",
"Drug C", "Drug D"), class = "factor"), pattern =
structure(c(1L,
1L, 4L, 4L, 4L, 3L, 3L, 3L, 3L, 2L, 2L, 5L, 5L, 5L, 5L, 5L), .Label = c("
Begin (A), Begin (B), End (B), End (A)",
" Begin (A, B), End (A, B)", " Begin (A, B), End (A, B), Begin
(C), End (C), Begin (D), End (D)",
" Begin (A, B, C), End (A, B), End (C)", "Begin (A, B, C), End
(A, B, C), Begin (C), Begin (D), End (C, D)"
), class = "factor"), start_drug = c(0, 0.7143, 0, 0, 0, 0, 0, 
14.5714, 25.4286, 0, 0, 0, 0, 0, 20, 18), stop_drug = c(21, 18, 
20, 20, 36, 7.429, 7.429, 21.857, 231.286, 35.286, 35.286, 17, 
17, 17, 32.8571, 32.8571)), .Names = c("profile_key",
"line",
"instance", "drug", "pattern",
"start_drug", "stop_drug"), row.names = c(NA,
-16L), class = "data.frame")

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

require(ggplot2)

temp <- TestData
TempData <- split(TestData, TestData$key_line)

for(temp in TempData){

png(filename = paste("plot", unique(temp$key_line), ".png",
sep = ""), width=600, height=300)

p <- ggplot(temp, aes(value, drug, fill = factor(instance))) + geom_line(size
= 6) + xlab("\n Time (Weeks)") + ylab("") + theme_bw() +
     opts(title = paste("Pattern = ", unique(temp$pattern), " \n
(profile_key = ", unique(temp$profile_key), ", line = ",
unique(temp$line), ") \n", sep = "")) +
     opts(legend.position="none")  
print(p)
dev.off()
}

Would like to add lines for written comments to the bottom of each graph. These
would look something like:

cat(
"Regimen 1:
__________________________________________________________",
"\n", "\n",
"Regimen 2:
__________________________________________________________",
"\n", "\n",
"Regimen 3:
__________________________________________________________",
"\n", "\n",
"Regimen 4:
__________________________________________________________",
"\n", "\n",
"Regimen 5:
__________________________________________________________",
"\n", "\n",
"Rationale:
__________________________________________________________",
"\n", "\n",
"          
__________________________________________________________",
"\n", "\n",
"          
__________________________________________________________",
"\n", "\n",
"          
__________________________________________________________",
"\n", "\n",
"          
__________________________________________________________",
"\n", "\n",
sep=""
)

Not sure exactly how one ought to approach this in R. Can it be done in one step
by adding to my ggplot2 code? Would it be better to do it using some sort of
post processing? Is it possible to add the text by placing what would be the
equivalent of a SAS put statement before the "dev.off()"?

Thanks,

Paul

Hi,

I would do the following,


library(ggplot2)
require(reshape)

TestData <- structure(list(profile_key = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2,
2, 3, 3, 3, 3, 3), line = c(1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2,
1, 1, 1, 1, 1), instance = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 2), drug = structure(c(1L, 2L, 1L, 2L, 3L, 1L, 2L,
3L, 4L, 1L, 2L, 2L, 1L, 3L, 4L, 3L), .Label = c("Drug A", "Drug
B",
"Drug C", "Drug D"), class = "factor"), pattern =
structure(c(1L,
1L, 4L, 4L, 4L, 3L, 3L, 3L, 3L, 2L, 2L, 5L, 5L, 5L, 5L, 5L), .Label c("
Begin (A), Begin (B), End (B), End (A)",
" Begin (A, B), End (A, B)", " Begin (A, B), End (A, B), Begin
(C),
End (C), Begin (D), End (D)",
" Begin (A, B, C), End (A, B), End (C)", "Begin (A, B, C), End
(A, B,
C), Begin (C), Begin (D), End (C, D)"
), class = "factor"), start_drug = c(0, 0.7143, 0, 0, 0, 0, 0,
14.5714, 25.4286, 0, 0, 0, 0, 0, 20, 18), stop_drug = c(21, 18,
20, 20, 36, 7.429, 7.429, 21.857, 231.286, 35.286, 35.286, 17,
17, 17, 32.8571, 32.8571)), .Names = c("profile_key",
"line",
"instance", "drug", "pattern",
"start_drug", "stop_drug"), row.names = c(NA,
-16L), class = "data.frame")

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 =
""))
str(TestData)

## wrapper to create one title
make_title <- function(d){
  with(d, paste("Pattern = ", unique(pattern),
                " \n (profile_key = ", unique(profile_key),
                ", line = ", unique(line), ") \n", sep =
""))
}

## create one plot given a sub-data.frame
make_plot <- function(d){
  ggplot(TestData, aes(value, drug, fill = factor(instance))) +
    geom_line(size = 6) + xlab("\n Time (Weeks)") + ylab("")
+ theme_bw()  +
      opts(title=make_title(d), legend.position="none")
}

library(plyr)
## apply the function to each subset and store in a list
plots <- dlply(TestData, "key_line", make_plot)

library(gridExtra)

annotation <- paste(
"Regimen 1:
__________________________________________________________",
"\n", "\n",
"Regimen 2:
__________________________________________________________",
"\n", "\n",
"Regimen 3:
__________________________________________________________",
"\n", "\n",
"Regimen 4:
__________________________________________________________",
"\n", "\n",
"Regimen 5:
__________________________________________________________",
"\n", "\n",
"Rationale:
__________________________________________________________",
"\n", "\n",
"          
__________________________________________________________",
"\n", "\n",
"          
__________________________________________________________",
"\n", "\n",
"          
__________________________________________________________",
"\n", "\n",
"          
__________________________________________________________",
"\n", "\n",
sep=""
)
## add annotation at the bottom ("subtitle")
make_annotation <- function(p, sub=textGrob(annotation, x=1, hjust=1.1)){
  arrangeGrob(p, sub=sub)
}

## apply annotations
plots_annotated <- llply(plots, make_annotation)

## print to multi-page pdf
pdf("multiple_pages.pdf", height=12, width=10)
print(plots_annotated)
dev.off()


HTH,

baptiste


On 31 March 2012 04:08, Paul Miller <pjmiller_57 at yahoo.com>
wrote:
> Hello All,
>
> Recently developed the code below for graphing patterns of chemotherapy
administration. As someone just starting to use R in their work, I managed to
figure out some parts of the code but needed help with others.
>
> setwd("N:/Regimen Coding/0906/Plots Test")
> getwd()
>
> TestData <- structure(list(profile_key = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2,
> 2, 3, 3, 3, 3, 3), line = c(1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2,
> 1, 1, 1, 1, 1), instance = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 2), drug = structure(c(1L, 2L, 1L, 2L, 3L, 1L, 2L,
> 3L, 4L, 1L, 2L, 2L, 1L, 3L, 4L, 3L), .Label = c("Drug A",
"Drug B",
> "Drug C", "Drug D"), class = "factor"),
pattern = structure(c(1L,
> 1L, 4L, 4L, 4L, 3L, 3L, 3L, 3L, 2L, 2L, 5L, 5L, 5L, 5L, 5L), .Label =
c(" Begin (A), Begin (B), End (B), End (A)",
> " Begin (A, B), End (A, B)", " Begin (A, B), End (A, B),
Begin (C), End (C), Begin (D), End (D)",
> " Begin (A, B, C), End (A, B), End (C)", "Begin (A, B, C),
End (A, B, C), Begin (C), Begin (D), End (C, D)"
> ), class = "factor"), start_drug = c(0, 0.7143, 0, 0, 0, 0, 0,
> 14.5714, 25.4286, 0, 0, 0, 0, 0, 20, 18), stop_drug = c(21, 18,
> 20, 20, 36, 7.429, 7.429, 21.857, 231.286, 35.286, 35.286, 17,
> 17, 17, 32.8571, 32.8571)), .Names = c("profile_key",
"line",
> "instance", "drug", "pattern",
"start_drug", "stop_drug"), row.names = c(NA,
> -16L), class = "data.frame")
>
> 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$key_line <- with(TestData,paste(profile_key, line, sep =
""))
> TestData
>
> require(ggplot2)
>
> temp <- TestData
> TempData <- split(TestData, TestData$key_line)
>
> for(temp in TempData){
>
> png(filename = paste("plot", unique(temp$key_line),
".png", sep = ""), width=600, height=300)
>
> p <- ggplot(temp, aes(value, drug, fill = factor(instance))) +
geom_line(size = 6) + xlab("\n Time (Weeks)") + ylab("") +
theme_bw() +
> ? ? opts(title = paste("Pattern = ", unique(temp$pattern), "
\n (profile_key = ", unique(temp$profile_key), ", line = ",
unique(temp$line), ") \n", sep = "")) +
> ? ? opts(legend.position="none")
> print(p)
> dev.off()
> }
>
> Would like to add lines for written comments to the bottom of each graph.
These would look something like:
>
> cat(
> "Regimen 1:
__________________________________________________________",
"\n", "\n",
> "Regimen 2:
__________________________________________________________",
"\n", "\n",
> "Regimen 3:
__________________________________________________________",
"\n", "\n",
> "Regimen 4:
__________________________________________________________",
"\n", "\n",
> "Regimen 5:
__________________________________________________________",
"\n", "\n",
> "Rationale:
__________________________________________________________",
"\n", "\n",
> " ? ? ? ? ?
__________________________________________________________",
"\n", "\n",
> " ? ? ? ? ?
__________________________________________________________",
"\n", "\n",
> " ? ? ? ? ?
__________________________________________________________",
"\n", "\n",
> " ? ? ? ? ?
__________________________________________________________",
"\n", "\n",
> sep=""
> )
>
> Not sure exactly how one ought to approach this in R. Can it be done in one
step by adding to my ggplot2 code? Would it be better to do it using some sort
of post processing? Is it possible to add the text by placing what would be the
equivalent of a SAS put statement before the "dev.off()"?
>
> Thanks,
>
> Paul
>
> ______________________________________________
> 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.

Hello Baptiste,

What you've done is very interesting. Went through and tried to understand
all the steps. Reminded me of studying languages in years gone by. Always found
it easier to read and understand a sentence than to construct a sentence of
one's own. This is particularly true when you're just learning.

Think I basically get it. You've got a function (make_title) that creates
the title for each graph. You've got another function (make_graph) that
actually creates each graph and gives it a title using the first function.
You're then applying the make_graph function to each value of key_line in
the TestData dataframe using dlply. dlply is being used instead of by() because
you want to start with a data frame and then end up with a list.

Next, you use a function called make_annotation to add the comment lines to each
graph. The make_annotation function uses arrangeGrob() from the gridExtra
package. You apply the function using llply this time because you are starting
out with a list and want to end up with a list.

Finally, you're outputting the annotated plots to the pdf destination which
can handle multiple plots if you specify "multiple_pages.pdf". This
seems a lot better than outputting individual graphs and then inserting them
into a Word document as I have been doing. The height and width of the page are
determined by the height and width options.

At this point, was hoping you could help with refining the output. I've
looked at the help page for pdf() and can't see how to modify the code in
the ways I'd like. Online searches and an examination of my various R books
haven't turned up?much either.
?
So here's what I'd like to do if possible:
?
1. Get the output to open at 100% magnification. This would be nice but
isn't all that important.
?
2. Add a document title to?the top of just the first page?(e.g., "Regimen
Patterns for Study X").
?
3. Add 1 inch margins around the page.
?
4. Make the comment lines roughly (or exactly) the same width as the graphs and
justify the text under the graphs.

5. Shrink the size of each graph/comment combination so it's possible to fit
two such combinations on a page.
?
Thanks,
?
Paul

Hi Baptiste,

Thanks for your help with this. Sorry for being slow to express my appreciation.
I had intended to put some more time into tweaking the graphs before responding.
Recently have been reading Hadley Wickham's ggplot2 book and have also
located some materials on the knitr package. Didn't get far enough in my
reading to do the necessary tweaking in a timely fashion though.

The result I'm getting now isn't perfect but it's still pretty
amazing. Certainly good enough for our internal coding exercise. Next steps will
be to add little grey extensions onto the bars and to obtain better control over
the sizing and placement of the graphs and comment text. The little grey
extensions will represent the time that chemotherapies remain active following
their final administration.

So far, the best way I've found for controlling the size of the graph is to
add to the number of comment lines. As it happens, we wanted more comment lines
anyway and so this worked out well. Must be a better way to get the necessary
control though. Will try to figure that out once I have more time.

Thanks again for your help with this.

Paul