Using rmarkdown with many plots created in a loop

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Using rmarkdown with many plots created in a loop

 I would appreciate some suggestions of a good way to prepare a report using rmarkdown, in which I loop through subsets of a data set, creating a plot of each subset, and interspersing among the figures some text relevant to each figure. One way is to have an R script write the rmd file, then render it. It works, but it's cumbersome and difficult to get the rmd syntax correct. I would very much appreciate suggestions for a better way. Reproducible example below. Thanks -Don Example data (other data structures could be used), and an example using this approach. myd <- lapply( 1:3,               function(i) list(df=data.frame(x=1:5, y=rnorm(5)),                                comment=paste('Data', LETTERS[i]))               ) Example interactive review (details would change depending on data structure) (I would typically insert pauses when working interactively) for (i in 1:3) {   cat(paste('Figure',i,'shows',myd[[i]]$comment),'\n') with(myd[[i]]$df , plot(x,y))   mtext(myd[[i]]$comment) mtext( paste(nrow(myd[[i]]$df),'points'), adj=1) }﻿ Note that along with the data I've saved some comments relevant to each subset. I've calculated them in the example data, but in general they could be completely arbitrary and come from anywhere. Now I'd like to get the same plots and comments into a report prepared using rmarkdown. Here's one way, having the loop create an rmd file, then rendering it. ### example script begins library(rmarkdown) myf <- 'myd.rmd' sink(myf) cat('--- title: Example --- Here are some figures with a comment appearing before each.\n\n' ) sink() for (i in 1:3) {   cat(paste('Figure',i,'comment:',myd[[i]]$comment),'\n', file=myf, append=TRUE) cat(" {r echo=FALSE, fig.cap='",paste('fig',i),"caption.'} with(myd[[",i,"]]$df , plot(x,y))   mtext(myd[[",i,"]]$comment) mtext( paste(nrow(myd[[",i,"]]$df),'points'), adj=1)  ", file=myf, append=TRUE)     } cat('Done with report\n', file=myf, append=TRUE) render(myf) -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 Lab cell 925-724-7509     ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
 Dear Don, Have a look at the knit_expand() function. Then you can create two Rmd files. One main file and one template file for the subsets. knit_expand() will find and replace anything between double curly brackets ("{{x}}" in the example below) with the value of the variable. The main file: --- title: "main" output: html_document --- {r setup, include=FALSE} library(knitr)  {r} mydf <- data.frame(   id = 1:4,   x = rnorm(100),   y = rnorm(100) )  {r} rmd <- sapply(   1:4,   function(x) {     knit_expand("child.Rmd", x = x)   } ) rmd <- paste(rmd, collapse = "\n") cat(rmd)  {r results = "asis"} rendered <- knit(text = rmd, quiet = TRUE) cat(rendered, sep = "\n")  The child.Rmd file ## ID {{x}} {r, fig.cap = "The caption: ID = {{x}}", echo = FALSE} i <- {{x}} detail <- subset(mydf, id == i) plot(x ~ y, data = detail)  Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance [hidden email] Havenlaan 88 bus 73, 1000 Brussel www.inbo.be /////////////////////////////////////////////////////////////////////////////////////////// To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey /////////////////////////////////////////////////////////////////////////////////////////// 2018-08-17 1:44 GMT+02:00 MacQueen, Don via R-help <[hidden email]>: > I would appreciate some suggestions of a good way to prepare a report > using rmarkdown, > in which I loop through subsets of a data set, creating a plot of each > subset, and interspersing > among the figures some text relevant to each figure. > > One way is to have an R script write the rmd file, then render it. > It works, but it's cumbersome and difficult to get the rmd syntax correct. > I would very much appreciate suggestions for a better way. > > Reproducible example below. > > Thanks > -Don > > > Example data (other data structures could be used), and an example using > this approach. > > myd <- lapply( 1:3, >               function(i) list(df=data.frame(x=1:5, y=rnorm(5)), >                                comment=paste('Data', LETTERS[i])) >               ) > > Example interactive review (details would change depending on data > structure) > (I would typically insert pauses when working interactively) > > for (i in 1:3) { >   cat(paste('Figure',i,'shows',myd[[i]]$comment),'\n') > with(myd[[i]]$df , plot(x,y)) >   mtext(myd[[i]]$comment) > mtext( paste(nrow(myd[[i]]$df),'points'), adj=1) > }﻿ > > Note that along with the data I've saved some comments relevant to each > subset. > I've calculated them in the example data, but in general they could be > completely > arbitrary and come from anywhere. > > Now I'd like to get the same plots and comments into a report prepared > using rmarkdown. > Here's one way, having the loop create an rmd file, then rendering it. > > ### example script begins > library(rmarkdown) > > myf <- 'myd.rmd' > sink(myf) > cat('--- > title: Example > --- > > Here are some figures with a comment appearing before each.\n\n' > ) > sink() > > for (i in 1:3) { >   cat(paste('Figure',i,'comment:',myd[[i]]$comment),'\n', file=myf, > append=TRUE) > > cat(" > {r echo=FALSE, fig.cap='",paste('fig',i),"caption.'} > with(myd[[",i,"]]$df , plot(x,y)) >   mtext(myd[[",i,"]]$comment) > mtext( paste(nrow(myd[[",i,"]]$df),'points'), adj=1) >  > ", file=myf, append=TRUE) > > } > > cat('Done with report\n', file=myf, append=TRUE) > > render(myf) > > -- > Don MacQueen > Lawrence Livermore National Laboratory > 7000 East Ave., L-627 > Livermore, CA 94550 > 925-423-1062 > Lab cell 925-724-7509 > > > > ______________________________________________ > [hidden email] mailing list -- To UNSUBSCRIBE and more, see > 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. >         [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
 In reply to this post by R help mailing list-2 ## Don, ## This is how I would approach the task of a set of coordinated plots. ## I would place individual plots inside a table.  The rows would index the ## datasets and there would be one or more data or description columns ## in addition to the column containing the graphs. ## I use the microplot package that I placed on CRAN about two years ago. ## install.packages("microplot") ## if necessary library(microplot) latexSetOptions() ## I normally use lattice.  microplot also works with ggplot or base graphics library(lattice) ## I placed your data into a single data.frame myd <- lapply( 1:3,               function(i) list(df=data.frame(x=1:5, y=rnorm(5)),                                comment=paste('Data', LETTERS[i]))               ) mydf <- cbind(group=rep(c("A", "B", "C"), each=5),               rbind(myd[[1]]$df, myd[[2]]$df, myd[[3]]$df)) mydf ## construct a lattice with multiple panels my.lattice <- xyplot(y ~ x | group, data=mydf, layout=c(1,3), as.table=TRUE, col="black", scales=list(alternating=FALSE), ylab=list(rot=1)) my.lattice ## microplot provides latex.trellis, which is a method for Hmisc::latex ## simplest display latex(my.lattice) ## now with comments and optional additional arguments mycomments <- c("Interesting Comment", "Full \\LaTeX\\ with an equation$e^{-x^2}$", "\\begin{tabular}{l}$\\frac{dy}{dx}$\\\\is interesting \\\\and has multiple lines\\end{tabular}") latex(my.lattice, title="Dataset", height.panel=1, width.panel=1.5, ## inches height.x.axis=.38, width.y.axis=.45, graph.header="xyplot(y ~ x | group)", dataobject=mycomments, colheads=c("Comments", "", "", "xyplot( y \\~{} x )"), caption="Very Interesting Caption", caption.loc="bottom", arraystretch=1.5) ## microplot produces MS Word tables as well as LaTeX tables. ## microplot works with ‘Sweave’, ‘knitr’, ‘emacs’ ‘orgmode’, and ‘rmarkdown’ ## Start with ?microplot-package ## and look at the demos and examples and vignette. ## Rich On Thu, Aug 16, 2018 at 7:44 PM, MacQueen, Don via R-help <[hidden email]> wrote: > I would appreciate some suggestions of a good way to prepare a report using rmarkdown, > in which I loop through subsets of a data set, creating a plot of each subset, and interspersing > among the figures some text relevant to each figure. > > One way is to have an R script write the rmd file, then render it. > It works, but it's cumbersome and difficult to get the rmd syntax correct. > I would very much appreciate suggestions for a better way. > > Reproducible example below. > > Thanks > -Don > > > Example data (other data structures could be used), and an example using this approach. > > myd <- lapply( 1:3, > function(i) list(df=data.frame(x=1:5, y=rnorm(5)), > comment=paste('Data', LETTERS[i])) > ) > > Example interactive review (details would change depending on data structure) > (I would typically insert pauses when working interactively) > > for (i in 1:3) { > cat(paste('Figure',i,'shows',myd[[i]]$comment),'\n') >   with(myd[[i]]$df , plot(x,y)) > mtext(myd[[i]]$comment) >   mtext( paste(nrow(myd[[i]]$df),'points'), adj=1) > }﻿ > > Note that along with the data I've saved some comments relevant to each subset. > I've calculated them in the example data, but in general they could be completely > arbitrary and come from anywhere. > > Now I'd like to get the same plots and comments into a report prepared using rmarkdown. > Here's one way, having the loop create an rmd file, then rendering it. > > ### example script begins > library(rmarkdown) > > myf <- 'myd.rmd' > sink(myf) > cat('--- > title: Example > --- > > Here are some figures with a comment appearing before each.\n\n' > ) > sink() > > for (i in 1:3) { > cat(paste('Figure',i,'comment:',myd[[i]]$comment),'\n', file=myf, append=TRUE) > >   cat(" > {r  echo=FALSE, fig.cap='",paste('fig',i),"caption.'} >   with(myd[[",i,"]]$df , plot(x,y)) > mtext(myd[[",i,"]]$comment) >   mtext( paste(nrow(myd[[",i,"]]\$df),'points'), adj=1) >  > ", file=myf, append=TRUE) > > } > > cat('Done with report\n', file=myf, append=TRUE) > > render(myf) > > -- > Don MacQueen > Lawrence Livermore National Laboratory > 7000 East Ave., L-627 > Livermore, CA 94550 > 925-423-1062 > Lab cell 925-724-7509 > > > > ______________________________________________ > [hidden email] mailing list -- To UNSUBSCRIBE and more, see > 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. ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.