[R] Adding text for written comments to bottom of graphs

[baptiste auguie]

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
>
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