microplot-package: Display microplots (sparklines) from R graphics panels in...

microplot-packageR Documentation

Display microplots (sparklines) from R graphics panels in tables in 'LaTeX', 'Word', 'HTML', 'Excel'.


The microplot function writes a set of R graphics files to be used as microplots (sparklines) in tables in either 'LaTeX', 'HTML', 'Word', or 'Excel' files. For 'LaTeX', we provide methods for the Hmisc::latex() generic function to construct 'latex' tabular environments which include the graphs. These can be used directly with the operating system 'pdflatex' or 'latex' command, or by using one of 'Sweave', 'knitr', 'rmarkdown', or 'Emacs org-mode' as an intermediary. For 'MS Word', the msWord() function uses the 'flextable' package to construct 'Word' tables which include the graphs. There are several distinct approaches for constructing HTML files. The simplest is to use the msWord() function with argument filetype="html". Alternatively, use either 'Emacs org-mode' or the htmlTable::htmlTable() function to construct an 'HTML' file containing tables which include the graphs. See the documentation for our as.htmlimg() function. For 'Excel' use on 'Windows', the file examples/irisExcel.xls includes 'VBA' code which brings the individual panels into individual cells in the spreadsheet. Examples in the examples and demo subdirectories are shown with 'lattice' graphics, 'ggplot2' graphics, and 'base' graphics. Examples for 'LaTeX' include 'Sweave' (both 'LaTeX'-style and 'Noweb'-style), 'knitr', 'emacs org-mode', and 'rmarkdown' input files and their 'pdf' output files. Examples for 'HTML' include 'org-mode' and 'Rmd' input files and their webarchive 'HTML' output files. In addition, the as.orgtable() function can display a data.frame in an 'org-mode' document. The examples for 'MS Word' (with either filetype="docx" or filetype="html") work with all operating systems. The package does not require the installation of 'LaTeX' or 'MS Word' to be able to write '.tex' or '.docx' files.


The DESCRIPTION file: This package was not yet installed at build time.
Index: This package was not yet installed at build time.

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, ggplot2, and base graphics. The tables can be targeted for display in 'LaTeX', 'MS Word' on any operating system, 'MS Excel' on 'Windows', or 'HTML'. We show examples of each.

The functions produce valid 'LaTeX' .tex files or 'Word' .docx files in the working directory. If 'LaTeX' or 'Word' are installed, then the generated files can be displayed on screen as illustrated in the help file examples and the demo directory. The .tex files can be \included in a larger .tex file. Or the generated .pdf file can be displayed in ‘LaTeX’ with an \includegraphics statement. The images in the displayed .docx file can be copied and pasted into a larger 'Word' file.

The best way to learn this package is to read the examples and demo files. The primary function microplot takes a trellis or ggplot object and generates a set of graphics files, one per panel of a multi-panel display. The latex and msWprd functions place the graphics files into a table.

The latex examples (in the help file examples) and demo files use the operating system pdflatex command with the 'R' pdf() or png() graphics device. Or they could use the operating system latex command with the 'R' ps() graphics device. They therefore require that the three options
all be set consistently. The recommended settings for pdflatex with pdf graphics files are included as the defaults in the function call
The recommended settings for latex with ps graphics files may be specified with the function call

Please see latexSetOptions for details on the recommended settings for use with the microplot package. See the "System options" section in the "Details" section of latex for discussion of the options themselves.

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

Most of the 'LaTeX' 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. An example in the demo directory 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. Each demo sets the options for pdfltex. Should you prefer latex you will need to run the demos manually. I recommend that you run the demos with ask=TRUE because will need to read them closely to see what they are doing.

To run the demos manually (with a stop at each graph), use

     demo("HowToUseMicroplot"         , package="microplot", ask=TRUE)
     demo("latex"                     , package="microplot", ask=TRUE)
     demo("latex-ggplot"              , package="microplot", ask=TRUE)
     demo("msWord"                    , package="microplot", ask=TRUE)
     demo("LegendrePolynomials"       , package="microplot", ask=TRUE)
     demo("timeseries"                , package="microplot", ask=TRUE)
     demo("NTplot"                    , package="microplot", ask=TRUE)
     demo("bwplot-lattice"            , package="microplot", ask=TRUE)
     demo("boxplot-ggplot"            , package="microplot", ask=TRUE)
     demo("tablesPlusGraphicColumn"   , package="microplot", ask=TRUE)
     demo("regrcoef"                  , package="microplot", ask=TRUE)
     demo("iris"                      , package="microplot", ask=TRUE)
     demo("AEdotplot"                 , package="microplot", ask=TRUE)
     demo("xtable"                    , package="microplot", ask=TRUE)
     demo("Examples"                  , package="microplot", ask=TRUE)

To run the demos automatically, with no stops, use ask=FALSE.

The examples directory 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.

The 'Excel' for Windows example is in file examples/irisExcel.xls. The 'VBA' code in that file shows how to place the individual microplots into 'Excel' cells.

See also the vignette:
vignette("rmhPoster", package="microplot")


Richard M. Heiberger, with contributions from Karen Byron and Nooreen Dabbish.

Maintainer: Richard M. Heiberger <rmh@temple.edu>

See Also

latex, latex.trellis, microplot, as.includegraphics


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

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

## Not run: 

  ## 0. set options for pdflatex and pdf graphics files

  ## 1. define dataset
  tmp <- matrix(rnorm(10), 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)))

  ## 2. lattice example for latex and msWord

  tmp.lattice <- lattice::bwplot(group ~ y | " " * group, data=tmp.df, layout=c(1,2),
                                 as.table=TRUE, xlim=c(-2.1, 1.3),
                                 scales=list(y=list(relation="free", at=NULL)))

  ## 3. using the latex.trellis method
        height.panel=.3, width.panel=3, ## inches
        x.axis=TRUE, y.axis=FALSE,
        rowlabel="group", caption="latex.trellis of lattice graph column")

  latex(tmp.lattice, dataobject=formatDF(tmp, dec=2),
        height.panel=.3, width.panel=1.5, ## inches
        x.axis=FALSE, y.axis=FALSE,
        rowlabel="group", caption="latex.trellis of numeric data and lattice graph column")

  ## 4. MS Word example.  Uses functions in the flextable and officer packages.

  tmplw.docx <-
    msWord(tmp.lattice, dataobject=format(tmp, digits=2),
           height.panel=.3, width.panel=2, ## inches
           height.x.axis=.35, width.y.axis=.3,
           rowlabel="group", width.rowname=.6,
           data.header="data values", width.dataobject=.6,
           caption="Lattice bwplot using msWord function")
  tmplw.docx  ## print method opens file
  ## cut and paste this graph into a larger .docx file.

  ## 5. ggplot2 example for latex and msWord


  tmpga.df <- cbind(tmp.df, fake="ff")
  tmpga <-
    ggplot(tmpga.df, aes(fake, y)) +
    geom_boxplot(outlier.size = 2) +
    facet_wrap(~ group, ncol=1) +
    coord_flip() + ylim(-2, 1.1)
  tmpga ## on interactive device

  ## 6. using the latex.ggplot method

  latex(tmpga, height.x.axis=.2, width.y.axis=.2, y.axis=FALSE)

  latex(tmpga, dataobject=formatDF(tmp, dec=2),
        height.panel=.5, height.x.axis=.2, width.y.axis=.2, y.axis=FALSE)

  ## 7. msWord with ggplot

  tmpga.docx <-
    msWord(tmpga, dataobject=format(tmp, digits=2),
           height.panel=.25, height.x.axis=.2, width.y.axis=.2, y.axis=FALSE,
           rowlabel="group", width.rowname=.6,
           data.header="data values", width.dataobject=.6,
           caption="ggplot2 boxplot using msWord function")
  tmpga.docx  ## print method opens file


  ## 8. base graphics example
  ## This must be done with an explicit loop because
  ## base graphics doesn't produce a graphics object.

  pdf("tmpb/fig%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 for horizontal plot
  boxplot(tmp["B",], horizontal=TRUE, ylim=range(tmp)) ## ylim for horizontal plot

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

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

  ## we are now using the latex.data.frame method in the Hmisc package
  tmpb.latex <- latex(tmpb.display, rowlabel="group",
                      caption="latex.default of base graphs")
  tmpb.latex$style <- "graphicx"
  tmpb.latex  ## this line requires latex in the PATH

  ## 9. detail for latex of lattice.  This is essentially what the
  ## latex.trellis method does all together.

  dir.verify("tmpl") ## create a new subdirectory of the working directory
  pdf("tmpl/fig%03d.pdf", onefile=FALSE, height=.5, width=2.5) ## inch
  update(tmp.lattice, layout=c(1,1), xlab="",

  tmpl.graphnames <- paste0("tmpl/fig", sprintf("%03i", 1:2), ".pdf")
  names(tmpl.graphnames) <- rownames(tmp)

  tmpl <-
  ## retains dimensions from pdf() statement
  tmpl.latex <- latex(tmpl, rowlabel="group",
                      caption="latex.default of lattice graph column")
  tmpl.latex  ## this line requires latex in the PATH

  tmplw <-
    data.frame(round(tmp, 2),
               graphs=as.includegraphics(tmpl.graphnames, width="1in"))
  ## retains aspect ratio from pdf() statement

  tmplw.latex <- latex(tmplw, rowlabel="group",
                       caption="latex.default of numeric data and lattice graph column")
  tmplw.latex$style <- "graphicx"
  tmplw.latex  ## this line requires latex in the PATH

  ## 10. detail for latex of ggplot.
  ## left as an exercise.  It is very similar to the detail for latex with lattice.

## End(Not run)

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

microplot documentation built on March 18, 2022, 7:56 p.m.