Sexpr[results=rd,stage=build]{tools:::Rd_package_title("microplot")}

Description

Details

The DESCRIPTION file: Sexpr[results=rd,stage=build]{tools:::Rd_package_DESCRIPTION("microplot")} Sexpr[results=rd,stage=build]{tools:::Rd_package_indices("microplot")}

Microplots are small plots that fit into the cells of a table that otherwise consists of text and numbers. A special case of a microplot is known as a sparkline.

The examples in this package show tables of simple or complex graphs placed into one or more columns of a table. The graphs can be produced by any graphical system in R. We show lattice, base, and ggplot2 graphics. The tables can be targeted for display in either LaTeX or HTML. We show both.

The best way to learn this package is to read the example and demo files.

This examples and demo files uses operating system latex command and the R pdf() graphics device. They therefore require that the three options
options()[c("latexcmd","dviExtension","xdvicmd")]
all be set to non-NULL values. Please see the "System options" in the "Details" section of
?Hmisc::latex for discussion of the options available.

I normally use the options
options(latexcmd="pdflatex")
options(dviExtension="pdf")
on Macintosh, on Windows, on Linux.

The "xdvicmd" option is dependent on details of the operating system. The goal is to name the function that opens pdf files. In order to open pdf files, the "xdvicmd" option must be specified. On systems I have looked, all these work
options(xdvicmd="open") ## Macintosh, Windows, SMP linux
options(xdvicmd="xdg-open") ## ubuntu linux
For anything else, you might need to experiment.

Should you prefer to use the operating system latex command to write dvi files, then leave the first two options unspecified. You might need to change the "xdvicmd". See ?Hmisc::latex for guidance. Also you will need to modify the examples to specify a different R device function instead of the pdf function used here.

The examples in this DESCRIPTION file are inside dontrun environments because they depend on options and write files. You must set the options for your system before running the example manually.

Most of the examples are shown using the Hmisc::latex function latex (I am coauthor of that function). The microplot package also works with the xtable::xtable function xtable. The last example in this help file shows a simple use of xtable

The demos in the demo directory are not inside a dontrun environment. You must set the options for your system before running them. I recommend that you run them manually, not automatically. You will need to read them closely to see what they are doing.

To run the demos automatically, use

demo("bwplot", package="microplot", ask=FALSE)

demo("NTplot", package="microplot", ask=FALSE)

demo("timeseries", package="microplot", ask=FALSE)

The examples directory paste0(system.file(package="microplot"), "/examples") includes complete working examples of Sweave (both LaTeX-style and Noweb-style), knitr, emacs orgmode, and rmarkdown input files and their pdf output files. These files must be copied into a directory in which you have write privilege, and that directory must be made the current working directory with setwd. They will not work from the installed package directory.

Author(s)

Maintainer: Sexpr[results=rd,stage=build]{tools:::Rd_package_maintainer("microplot")}

See Also

latex

Examples

## Not run: 
latexCheckOptions()

## These are the LaTeX options I use
options(latexcmd="pdflatex") ## Macintosh, Windows, linux
options(dviExtension="pdf")  ## Macintosh, Windows, linux

options(xdvicmd="open")      ## Macintosh, Windows, SMP linux
## or
options(xdvicmd="xdg-open")  ## ubuntu linux

## See ?Hmisc::latex for discussion of these options.

## End(Not run)


## This example writes a set of pdf files and then uses the Hmisc::latex
## function to display them in LaTeX.

## The graphs are constructed three times, once each with lattice,
## base graphics, and ggplot2.

## Not run: 
  tmp <- matrix(rnorm(20), 2, 5, byrow=TRUE,
                dimnames=list(c("A", "B"), paste0("X", 1:5)))

  tmp.df <- data.frame(y=as.vector(t(tmp)),
                      group=factor(rep(row.names(tmp), each=5)))
  tmp.df

## End(Not run)

  ## All three examples use the pdf device

  ## lattice example
## Not run: 

  library(lattice)

  tmp.lattice <- bwplot(group ~ y | group, data=tmp.df, layout=c(1,2))
  tmp.lattice

  pdf("tmpl%03d.pdf", onefile=FALSE, height=.4, width=4) ## inch
  update(tmp.lattice, layout=c(1,1), xlab=NULL, ylab=NULL,
         par.settings=list(layout.heights=layoutHeightsCollapse(),
                           layout.widths=layoutWidthsCollapse(),
                           axis.line=list(col="transparent")),
         scales=list(y=list(relation="free", at=NULL)))
  dev.off()

  tmpl.graphnames <- paste0("tmpl", sprintf("%03i", 1:2), ".pdf")

  tmpl.display <- data.frame(round(tmp, 2),
                             graphs=as.includegraphics(tmpl.graphnames, raise="-.55ex"))
  tmpl.display

  tmpl.latex <- Hmisc::latex(tmpl.display)
  tmpl.latex$style <- "graphicx"
  tmpl.latex  ## this line requires latex in the PATH, and Hmisc to be loaded
  ## Hmisc::print.latex(tmpl.latex) ## if Hmisc is not loaded


## End(Not run)

## base graphics example
## Not run: 

  pdf("tmpb%03d.pdf", onefile=FALSE, height=.5, width=3) ## inch
  par( bty="n", xaxt="n", omd=c(0,1, 0,1), mai=c(0,0,0,0))
  boxplot(tmp["A",], horizontal=TRUE, ylim=range(tmp)) ## ylim is correct for horizontal plot
  boxplot(tmp["B",], horizontal=TRUE, ylim=range(tmp)) ## ylim is correct for horizontal plot
  dev.off()

  tmpb.graphnames <- paste0("tmpb", sprintf("%03i", 1:2), ".pdf")

  tmpb.display <-
    data.frame(round(tmp, 2),
               graphs=as.includegraphics(tmpb.graphnames, height="2em", raise="-1.4ex"))
  tmpb.display

  tmpb.latex <- Hmisc::latex(tmpb.display)
  tmpb.latex$style <- "graphicx"
  tmpb.latex  ## this line requires latex in the PATH, and Hmisc to be loaded
  ## Hmisc::print.latex(tmpb.latex) ## if Hmisc is not loaded


## End(Not run)

## ggplot2 example, whole set constructed as a unit, then printed one panel at a time.
## Not run: 

  library(ggplot2)
  tmpga <-
    ggplot(tmp.df, aes(group, y)) +
      geom_boxplot(outlier.size = 8) +
        coord_flip() +
          theme_collapse()
  tmpga ## on interactive device

  pdf("tmpga%03d.pdf", onefile=FALSE, height=1, width=4) ## inch
  for (i in 1:length(levels(tmp.df$group))) {
    tmpga$coordinates$limits$x <- c(i, i)  ## I dislike this usage.
                                        ## I want to use "+" with some ggplot2 function,
          ## but have not figured out the right incantation.
    print(tmpga)
  }
  dev.off()

  graphnames <- paste0("tmpga", sprintf("%03i", 1:2), ".pdf")

  tmpga.display <- data.frame(round(tmp, 2),
                            graphs=as.includegraphics(graphnames, raise="-.7ex"))
  tmpga.display

  tmpga.latex <- Hmisc::latex(tmpga.display)
  tmpga.latex$style <- "graphicx"
  tmpga.latex  ## this line requires latex in the PATH, and Hmisc to be loaded
  ## Hmisc::print.latex(tmpga.latex) ## if Hmisc is not loaded


## End(Not run)

## ggplot2 example, constructed one panel at a time.
## Not run: 

  library(ggplot2)

  pdf("tmpgb%03d.pdf", onefile=FALSE, height=1, width=4) ## inch
  ggplot(tmp.df[1:5,], aes(group, y)) +
    geom_boxplot(outlier.size = 8) + ylim(range(tmp.df[,1])) +
      coord_flip() +
        theme_collapse()
  ggplot(tmp.df[6:10,], aes(group, y)) +
    geom_boxplot() + ylim(range(tmp.df[,1])) +
      coord_flip() +
        theme_collapse()
  dev.off()

  graphnames <- paste0("tmpgb", sprintf("%03i", 1:2), ".pdf")

  tmpgb.display <- data.frame(round(tmp, 2),
                            graphs=as.includegraphics(graphnames, raise="-.7ex"))
  tmpgb.display

  tmpgb.latex <- Hmisc::latex(tmpgb.display)
  tmpgb.latex$style <- "graphicx"
  tmpgb.latex  ## this line requires latex in the PATH, and Hmisc to be loaded
  ## Hmisc::print.latex(tmpgb.latex) ## if Hmisc is not loaded


## End(Not run)

## xtable example
## Not run: 
  tmpl.display ## from lattice example above
  tmplx.name <- "tmpldisplayxtable.tex"
  print(xtable::xtable(tmpl.display),
        caption.placement = "top",
	sanitize.text.function = function(x) x,  ## xtable converts "abc" to "$ackslash$abc"
        file=tmplx.name)                         ## sanitize restores it back to "abc".
  tmpx.latex <- list(file=tmplx.name, style="graphicx")
  class(tmpx.latex) <- "latex"

  tmpx.latex  ## this line requires latex in the PATH, and Hmisc to be loaded
  ## Hmisc::print.latex(tmpx.latex) ## if Hmisc is not loaded

## End(Not run)


## Please see the demos for more interesting examples.
##xs demo(package="microplot")

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