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...@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@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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