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Exporting Data From R

Sun, 10 Apr 2016 18:01:37 +0200

In the previous chapters we described the essentials of R programming as well as how to import data into R. Here, you’ll learn how to export data from R to txt, csv, Excel (xls, xlsx) and R data file formats. Additionally, we’ll describe how to create and format Word and PowerPoint documents from R.

Export Data From R to txt|csv|Excel files
Create and format word and powerpoint documents using R and ReporteRs package:

Writing data from R to a txt|csv file: R base functions

R base functions for writing data: write.table(), write.csv(), write.csv2()
Writing data to a file

# Loading mtcars data
data("mtcars")

# Write data to txt file: tab separated values
# sep = "\t"
write.table(mtcars, file = "mtcars.txt", sep = "\t",
            row.names = TRUE, col.names = NA)

# Write data to csv files:  
# decimal point = "." and value separators = comma (",")
write.csv(mtcars, file = "mtcars.csv")

# Write data to csv files: 
# decimal point = comma (",") and value separators = semicolon (";")
write.csv2(mtcars, file = "mtcars.csv")

Fast writing of Data From R to txt|csv Files: readr package

Installing and loading readr: install.packages(“readr”)
readr functions for writing data: write_tsv(), write_csv()
Writing data to a file

# Loading mtcars data
data("mtcars")

library("readr")
# Writing mtcars data to a tsv file
write_tsv(mtcars, path = "mtcars.txt")

# Writing mtcars data to a csv file
write_csv(mtcars, path = "mtcars.csv")

Writing data from R to Excel files (xls|xlsx)

Installing xlsx package: install.packages(“xlsx”)
Using xlsx package: write.xlsx()

library("xlsx")

# Write the first data set in a new workbook
write.xlsx(USArrests, file = "myworkbook.xlsx",
      sheetName = "USA-ARRESTS", append = FALSE)

# Add a second data set in a new worksheet
write.xlsx(mtcars, file = "myworkbook.xlsx", 
           sheetName="MTCARS", append=TRUE)

Saving data into R data format: RDATA and RDS

Save one object to a file: saveRDS(object, file), readRDS(file)
Save multiple objects to a file: save(data1, data2, file), load(file)
Save your entire workspace: save.image(), load()

Saving and restoring one single R object:

# Save a single object to a file
saveRDS(mtcars, "mtcars.rds")

# Restore it under a different name
my_data <- readRDS("mtcars.rds")

Saving and restoring one or more R objects:

# Save multiple objects
save(data1, data2, file = "data.RData")

# To load the data again
load("data.RData")

Saving and restoring your entire workspace:

# Save your workspace
save.image(file = "my_work_space.RData")

# Load the workspace again
load("my_work_space.RData")

Create and format Word documents with R and ReporteRs package

ReporteRs package, by David Gohel, provides easy to use functions to write and format Word documents. It can be also used to generate Word document from a template file with logos, fonts, etc. ReporteRs is Java-based solution, so it works on Windows, Linux and Mac OS systems.

Install and load the ReporteRs R package
Create a simple Word document
- Add texts : title and paragraphs of texts
- Format the text of a Word document using R software
- Add plots and images
- Add a table
- Add lists : ordered and unordered lists
- Add a footnote to a Word document
- Add R scripts
Add a table of contents into a Word document

Create a Word document from a template file with R and ReporteRs package

Quick introduction to ReporteRs package
Create a Word document using a template file

Add a table into a Word document with R and ReporteRs package

Add a simple table
Add a formatted table
- Change the background colors of rows and columns
- Change cell background and text colors
- Insert content into a table : header and footer rows
Analyze, format and export a correlation matrix into a Word document
Powerpoint

Create and format PowerPoint documents with R and ReporteRs

Why is it important to be able to generate a PowerPoint report from R ?
- Reason I : Many collaborators works with Microsoft office tools
- Reason II : keeping beautiful R graphs beautiful for publications
Install and load the ReporteRs package
Create a simple PowerPoint document
- Slide layout
- Generate a simple PowerPoint document from R software
- Format the text of a PowerPoint document
- Add plots and images
- Add a table
- Add ordered and unordered lists
Create a PowerPoint document from a template file

Create an editable graph from R to PowerPoint

Case of base graphs
Case of graphs generated using ggplot2

Create and format PowerPoint documents from R software

Sat, 09 Apr 2016 10:28:43 +0200

Why is it important to be able to generate a PowerPoint report from R ?

There are at least, two reasons for this, as described in the next sections.

Reason I : Many collaborators works with Microsoft office tools

About 1 billion people worldwide use Microsoft Office (1 in 7 people on the planet; source: Microsoft).

Furthermore, many collaborators still working with MS Office software (Word, PowerPoint, Excel) for :

editing their text and tracking changes
copy-pasting texts, images and tables from multiple sources
saving and analyzing their data

In this context, a report generated as a PDF or HTMl files is less useful with some collaborators.

Reason II : keeping beautiful R graphs beautifull for publications

R plots can be customized to be as beautiful as your imagination can make them. Unfortunately, preserving this beauty is not always an easy task when you want to publish these graphs or show them in a professional presentations.

Yes, this problem can be solved using knitr/rmarkdown/Latex/Beamer/Slidify. However, it would be very difficult to remake the whole presentation in a different format. Furthermore, many journals don’t accept Latex documents.

(source).

But wasn’t this problem solved already?

The answer of this question is yes and no. There have been several attempts to solve this problem, but many of them are not easy to use.

One of the previous solutions is R2PPT package. Unfortunately R2PPT is available for Windows OS only and it depends on rcom or RDCOMClient for generating Microsoft PowerPoint presentations.

Objective

The goal of this R tutorial is to show you how to easily and quickly, format and export R outputs (including data tables, plots, paragraphs of text and R scripts) from R statistical software to a Microsoft PowerPoint document (.pptx file format) using ReporteRs package.

ReporteRs is a Java-based solution, so it works on Windows, Mac and Linux.

Install and load the ReporteRs package

Use the R code below :

install.packages('ReporteRs') # Install
library('ReporteRs') # Load

Note that ReporteRs relies on Java (>= 1.6) ; make sure you have an installed JRE

The version of Java installed on your computer, can be checked as follow :

system("java -version")

Create a simple PowerPoint document

Four simple steps are required :

Use the pptx() function to create a PowerPoint object.
Use the addSlide() function to add a slide into the PowerPoint document.
Add contents into the created slide using the functions below :
- addTitle: Add a title
- addParagraph: Add paragraphs of text
- addFlexTable: Add a table
- addPlot: Add a plot generated in R
- addImage: Add external images
- addRScript: Highlight and add R code
- addDate : Add a date
- addPageNumber : Add a page number
- AddFooter : Add a footer
Write the document into a .pptx file using writeDoc() function

Slide layout

Before showing you an example of how to create and format PowerPoint from R Software, let’s first discuss about slide layout. This is very important to understand the examples provided in this tutorial.

When creating a new slide, you should specify the layout of the slide. The available layouts in the “MS Office PowerPoint” (default template, on my computer) are illustrated in the figure below :

addSlide() function can be used to add a new slide into a PowerPoint document from R software. A simplified format of the function is :

doc <- addSlide(doc, slide.layout)

doc : a pptx object where slide has to be added
slide.layout : the layout to use for the slide.

Among the possible values for the argument slide.layout, there are : “Title Slide”, “Title and Content”, “Two Content”, “Section Header”, “Content with Caption”, “Title Only”, “Comparison”.

However, you should use only the available slide layouts in your computer.

To view the slide layouts available in your computer, use the R code below :

library(ReporteRs)
doc = pptx()
slide.layouts(doc)

 [1] "Title Slide"             "Title and Vertical Text" "Title and Content"       "Two Content"            
 [5] "Section Header"          "Vertical Title and Text" "Content with Caption"    "Title Only"             
 [9] "Comparison"              "Blank"

These layouts are illustrated below :

doc <- pptx()
layouts <-slide.layouts(doc) # All available layout
#  plot each slide style
for(i in layouts ){
  par(mar=c(0.5,0.5,2,0.5), cex=0.7)
  slide.layouts(doc, i )
    title(main = paste0("'", i, "'" ))
  if(interactive()) readline(prompt = "Show next slide layout")
}

Note that, the selected layout determines the contents you can add into the slide (See the figure above).

Example 1 - If you choose ‘Title and Content’ as a slide layout, you can add only :
- a title
- and one content which can be texts, plots, images, tables or R code
Example 2 - If you choose ‘Two Content’ as a slide layout, you can add :
- a title
- and two contents : For example, you can add a table in the left panel and a paragraph of texts in the right panel.
Example 3 - If you choose ‘Comparison’, you can add a title and four contents (plots, tables, paragraphs, images)

Whatever the slide layout chosen, you can use the functions addDate(), addFooter() and addPageNumber() to add date, footer and slide number, respectively.

Generate a simple PowerPoint document from R software

The R code below creates a PowerPoint document with a title slide, plots, tables, and an R script :

library( ReporteRs )

# Create a PowerPoint document
doc = pptx( )

# Slide 1 : Title slide
#+++++++++++++++++++++++
doc <- addSlide(doc, "Title Slide")
doc <- addTitle(doc,"Create a PowerPoint document from R software")
doc <- addSubtitle(doc, "R and ReporteRs package")
doc <- addDate(doc)
doc <- addFooter(doc, "Isaac Newton")
doc <- addPageNumber(doc, "1/4")

# Slide 2 : Add plot
#+++++++++++++++++++++++
doc <- addSlide(doc, "Title and Content")
doc <- addTitle(doc, "Bar plot")
plotFunc<- function(){
  barplot(VADeaths, beside = TRUE,
          col = c("lightblue", "mistyrose", "lightcyan",
                  "lavender", "cornsilk"),
  legend = rownames(VADeaths), ylim = c(0, 100))
  title(main = "Death Rates in Virginia", font.main = 4)
}
doc <- addPlot(doc, plotFunc )
doc <- addPageNumber(doc, "2/4")

# Slide 3 : Add table 
#+++++++++++++++++++++++
doc <- addSlide(doc, "Two Content")
doc <- addTitle(doc,"iris data sets")
doc <- addFlexTable(doc, FlexTable(iris[1:10,] ))
doc <- addParagraph(doc, "iris data set gives the measurements in centimeters of the variables sepal length and width and petal length and width, respectively, for 50 flowers from each of 3 species of iris. The species are Iris setosa, versicolor, and virginica.")
doc <- addPageNumber(doc, "3/4")

# Silde 4 : Add R script
#+++++++++++++++++++++
doc <- addSlide(doc, "Content with Caption")
doc <- addTitle(doc, "R Script for histogram plot")
doc <- addPlot(doc, function() hist(iris$Sepal.Width, col=4))
r_code ="data(iris)
hist(iris$Sepal.Width, col = 4)"
doc <- addRScript(doc, text=r_code)

# write the document 
writeDoc(doc, "r-reporters-powerpoint.pptx" )

The PowerPoint document created by the R code above is available here : R software and ReporteRs package - Example of creating a PowerPoint document

Note that, you can use addPageNumber() function without specifying the value of the slide number, as follow :

doc <- addPageNumber(doc)

In this case slide number is added using the default setting (e.g : 1 for slide1, 2 for slide 2).

If you want to customize the numbering, use the function as follow :

doc <- addPageNumber(doc, "1/2") # Example 1
doc <- addPageNumber(doc, "I") # Example 2

Format the text of a PowerPoint document

Text properties : font, color and size

As illustrated in the figure below, text properties include :

Font : family (e.g : “Arial”), size (e.g : 11), style (e.g : “italic”)
Underlined text
Color (e.g : “blue”)
Vertical align (superscript, subscript)

The default font size and font family of the PowerPoint can be modified as follow :

options( "ReporteRs-fontsize" = 18, 
         "ReporteRs-default-font" = "Arial")

Change the appearance of a “Piece Of Text” (pot)

The function pot() [Pieces Of Text] is used to modify the appearance of a text. It can be used also to create a hyperlink. The format is :

pot(value="", format = textProperties())

value : the text to be formatted
format : the properties to use for formatting the text

The allowed values for the argument format are the following functions :

textProperties() : the text formatting properties
textBold(), textItalic(), textBoldItalic() and textNormal() which are shortcuts for bold, italic, bold-italic and normal text, respectively.

These functions can take the arguments below :

color : font color; e.g : color=“#000000” or color = “black”.
font.size : a integer indicating the font size.
font.weight : the font weight. Possible values are “normal” or “bold”.
font.style : the font style. Possible values are “normal” or “italic”.
underlined : a logical value specifying if the text should be underlined.
font.family : the font family; e.g : “Arial”.
vertical.align : a character indicating font vertical alignments. Expected values are “baseline”" or “subscript” or “superscript”. Default value is baseline.
shading.color : background color of the text (e.g “#000000” or “black”)

The R code below creates a PowerPoint document containing a formatted text and a hyperlink :

library( ReporteRs )

# Change the default font size and font family
options('ReporteRs-fontsize'= 18, 'ReporteRs-default-font'='Arial')

doc = pptx( )

doc <- addSlide(doc, "Two Content")
doc <- addTitle(doc,"Document with formatted texts")
doc <- addFlexTable(doc, FlexTable(iris[1:10,] ))

my_text <- pot("iris data set", textBold(color = "blue"))+
          " contains the measurements of " + 
          pot("sepal length", textBold(color="red"))+ 
        " and width and petal length and width"
  
my_link <- pot('Click here to visit STHDA web site!', 
    hyperlink = 'https://www.sthda.com/english',
    format=textBoldItalic(color = 'blue', underline = TRUE ))

doc <- addParagraph(doc, 
      value = set_of_paragraphs(my_text, " ",  my_link),
     par.properties=parProperties(text.align="justify")
    )

writeDoc(doc, "r-reporters-powerpoint-formatted.pptx" )

Add plots and images

The functions addPlot() and addImage() can be used for adding a plot or an external image to the document. addPlot() works with all R plots (base graphics, lattice, ggplot2 and grid).

These two functions can be used as follow :

# Add plots
# fun : R plotting function
# ... : other arguments to pass to the plotting function
addPlot(doc, fun, ...)

# Add images
# filename : path to the external image
addImage(doc, filename)

The R code below creates a PowerPoint document containing a histogram and an image (downloaded from R website) :

library( ReporteRs )

doc = pptx()

# Slide 1 : Title slide
doc <- addSlide(doc, "Title Slide")
doc <- addTitle(doc,"Document containing plots and images")
doc <- addSubtitle(doc, "R and ReporteRs package")

# Slide 2 : Add plot
doc <- addSlide(doc, "Two Content")
doc <- addTitle(doc,"Histogram plot")
doc <- addPlot(doc, function() hist(iris$Sepal.Width, col="lightblue"))
doc <- addParagraph(doc, "This histogram is generated using iris data sets")

# Slide 3 : Add  an image
# download an image from R website
download.file(url="http://www.r-project.org/hpgraphic.png",
              destfile="r-home-image.png", quiet=TRUE)
doc <- addSlide(doc, "Two Content")
doc <- addTitle(doc,"Image from R website")
doc <- addImage(doc, "r-home-image.png")
doc <- addParagraph(doc, "This image has been downloaded from R website")
 
writeDoc(doc, "r-reporters-powerpoint-plot-image.pptx")

The PowerPoint document created by the R code above is available here : R software and ReporteRs package - PowerPoint document containing plots and images

Note that, addPlot() function can take other arguments such as pointsize to change the size of plotted texts (default value is 12; in pixels)
For addImage() function, the allowed file formats are PNG, WMF, JPEG and GIF images..

Add a table

addFlexTable() function is used to format and add a table into the PowerPoint.

It can be used as follow :

STEP 1 : Create a table using FlexTable() or vanilla.table() function. These two functions generate a ‘flexible’ table which can be easily formatted before adding into the slide.
STEP 2 : Add the create table into the document using addFlexTable() function as follow :

# doc : pptx object
# flextable : FlexTable object

# Example 1
doc <- addFlexTable(doc, flextable = FlexTable(data))

# Example 2 
doc <- addFlexTable(doc, flextable = vanilla.table(data))

setZebraStyle() function can be used to color odd and even rows differently; for example, odd rows in gray color and even rows in white color.

The example below creates a PowerPoint document with 3 slides containing a simple table (slide 1), vanilla table (slide 2) and a zebra striped table (slide 3) :

doc = pptx()

data<-iris[1:5, ]

# Slide 1 : Simple table
doc <- addSlide(doc, "Title and Content")
doc <- addTitle(doc,"Simple table")
doc <- addFlexTable(doc, FlexTable(data))

# Slide 2 : vanilla table
doc <- addSlide(doc, "Title and Content")
doc <- addTitle(doc,"Vanilla table")
doc <- addFlexTable(doc, vanilla.table(data))

# Slide 3 : Zebra striped table
doc <- addSlide(doc, "Title and Content")
doc <- addTitle(doc,"Zebra striped table")
MyFTable <- vanilla.table(data)
MyFTable <- setZebraStyle(MyFTable, odd = '#eeeeee', even = 'white')
doc <- addFlexTable( doc, MyFTable)

writeDoc(doc, "r-reporters-powerpoint-add-table.pptx")

The PowerPoint document created by the R code above is available here : R software and ReporteRs package - PowerPoint document containing tables

Add ordered and unordered lists

Lists can be added using addParagraph() function as follow :

doc  <- addParagraph(doc, 
  value = c('Item 1', "Item 2", "Item 3")
  par.properties = parProperties(list.style = 'ordered', level = 1 )

value : a set of items to be added as a list
par.properties : the paragraph formatting properties. It takes list.style and level as arguments :
- list.style : possible values are ‘unordered’ and ‘ordered’
- level : a numeric value indicating the level of the item to be added in the list

The example below generates a one-slide PowerPoint document containing an ordered and unordered lists :

doc <- pptx()

doc <- addSlide(doc, "Two Content")
doc <- addTitle(doc, "Ordered and unordored lists")

# 1. Ordered list
doc <- addParagraph(doc, value= c("Item 1", "Item 2", "Item 3"),
          par.properties =  parProperties(list.style = 'ordered'))

# 2. Unordered list
doc <- addParagraph(doc, value= c("Item 1", "Item 2", "Item 3"),
          par.properties =  parProperties(list.style = 'unordered'))

writeDoc(doc, file = "r-reporters-powerpoint-lists.pptx")

Create a PowerPoint document from a template file

This approach is useful in many situations :

If you work in a corporate environment and you want to generate a PowerPoint document based on a template with specific fonts, color, logos, etc.
If you want to modify and insert new contents into an existing PowerPoint document.
If you want to use text formatting styles and slide layouts from a given template file.

Note that, if you use a template file to create a PowerPoint document, slide layouts are those available in the template.

A template file can be specified to the pptx() function as follow :

# Create a PowerPoint document
doc <- pptx(template="path/to/your/powerpoint/template/file.pptx")

# ...............
# Add contents
# ...............

# Write the PowerPoint document to a file 
writeDoc(doc, file = "output-file.pptx")

In the next section We’ll :

download a PowerPoint template file from STHDA website
Check the available slide layouts in the template file
Create a PowerPoint document based on the template

Download a template file

# Download a PowerPoint template file from STHDA website
download.file(url="https://www.sthda.com/sthda/RDoc/example-files/r-reporters-powerpoint-template.pptx",
    destfile="r-reporters-powerpoint-template.pptx", quiet=TRUE)

Slide layouts available in the template file

You can use one of the layout below when adding a new slide into the PowerPoint :

doc <- pptx(template="r-reporters-powerpoint-template.pptx")
layouts <-slide.layouts(doc) # All available layout
# Plot the layouts
for(i in layouts ){
  par(mar=c(0.5,0.5,2,0.5), cex=0.7)
  slide.layouts(doc, i )
  title(main = paste0("'", i, "'" ))
  if(interactive()) readline(prompt = "Show next slide layout")
}

Create a PowerPoint document from the template file

Note that, the template file contains already one empty slide which can be removed manually.

library( ReporteRs )

# Download a PowerPoint template file from STHDA website
download.file(url="https://www.sthda.com/sthda/RDoc/example-files/r-reporters-powerpoint-template.pptx",
    destfile="r-reporters-powerpoint-template.pptx", quiet=TRUE)

options('ReporteRs-fontsize'= 18, 'ReporteRs-default-font'='Arial')

doc <- pptx(template="r-reporters-powerpoint-template.pptx" )

# Slide 1 : Title slide
#+++++++++++++++++++++++
doc <- addSlide(doc, "Title Slide")
doc <- addTitle(doc,"Create a PowerPoint from template using R software")
doc <- addSubtitle(doc, "R and ReporteRs package")
doc <- addDate(doc)
doc <- addFooter(doc, "Isaac Newton")
doc <- addPageNumber(doc, "1/4")

# Slide 2 : Add plot
#+++++++++++++++++++++++
doc <- addSlide(doc, "Title and Content")
doc <- addTitle(doc, "Bar plot")
plotFunc<- function(){
  barplot(VADeaths, beside = TRUE,
          col = c("lightblue", "mistyrose", "lightcyan",
                  "lavender", "cornsilk"),
  legend = rownames(VADeaths), ylim = c(0, 100))
  title(main = "Death Rates in Virginia", font.main = 4)
}
doc <- addPlot(doc, plotFunc )
doc <- addPageNumber(doc, "2/4")

# Slide 3 : Add table 
#+++++++++++++++++++++++
doc <- addSlide(doc, "Two Content")
doc <- addTitle(doc,"iris data sets")
doc <- addFlexTable(doc, FlexTable(iris[1:4,] ))
doc <- addParagraph(doc, "iris data set gives the measurements in centimeters of the variables sepal length and width and petal length and width, respectively, for 50 flowers from each of 3 species of iris. The species are Iris setosa, versicolor, and virginica.")
doc <- addPageNumber(doc, "3/4")

# Silde 4 : Add R script
#+++++++++++++++++++++
doc <- addSlide(doc, "Content with Caption")
doc <- addTitle(doc, "R Script for histogram plot")
doc <- addPlot(doc, function() hist(iris$Sepal.Width, col=4))
r_code ="data(iris)
hist(iris$Sepal.Width, col = 4)"
doc <- addRScript(doc, text=r_code)

# write the document 
writeDoc(doc, "r-reporters-powerpoint-from-template.pptx" )

The PowerPoint document created by the R code above is available here : R software and ReporteRs package - PowerPoint document from template

Infos

This analysis has been performed using R (ver. 3.1.0).

You can read more about ReporteRs and download the source code at the following link :

GitHub (David Gohel): ReporteRs

Create an editable graph from R software

Sat, 09 Apr 2016 10:27:57 +0200

Who is this article for ?
What R package to use ?
Create editable plots
- Case of base graphs
- Case of graphes generated using ggplot2
Infos

In this article you’ll learn how to create an editable vector graphics from R software. This could be interesting in some cases and gives you the ability to edit your graphics from PowerPoint. You can change line types, colors, point shapes, etc, …

Who is this article for ?

If you want to export your plot from R to PowerPoint automatically, this is for you.

If you want to bring your ggplot2 charts to PowerPoint, then this guide is for you.

If you’re looking for an exact package to create an editable plot and to save it as a PowerPoint document, then you’ll love this tutorial.

If you’re a beginner in R programming, you’ll definitely learn something new that you can use if needed.

What R package to use ?

Editable vector graphics can be created and saved in a PowerPoint document using ReporteRs package.

Install and load the package as follow :

install.packages('ReporteRs') # Install
library('ReporteRs') # Load

Create editable plots

Case of base graphs

The example below creates a PowerPoint document in your current working directory. The document contains one slide with 2 panels :

The first panel contains an editable box plot
The second panel contains a raster format

The PowerPoint document created by the R code below is available here : R software and ReporteRs package - create an editable base graph

library('ReporteRs')
# Create a new powerpoint document
doc <- pptx()

# Add a new slide into the ppt document 
doc <- addSlide(doc, "Two Content" )

# add a slide title
doc<- addTitle(doc, "Editable vector graphics format versus raster format" )

# A function for creating a box plot
boxplotFunc<- function(){
      boxplot(len ~ dose, data = ToothGrowth, 
        col=2:4,main = "Guinea Pigs' Tooth Growth",
        xlab = "Vitamin C dose mg",
        ylab = "tooth length")
      }

# Add an editable box plot
doc <- addPlot(doc, boxplotFunc, vector.graphic = TRUE )

# Add a raster box plot
doc <- addPlot(doc, boxplotFunc, vector.graphic = FALSE )

# write the document to a file
writeDoc(doc, file = "editable-graph.pptx")

Open the created PowerPoint and try to edit the first box plot by changing the fill colors, line types, etc…

Case of graphs generated using ggplot2

ggplot2 is a powerful R package, implemented by Hadley Wickham, for producing a visually appealing charts.

Install and load it as follow :

install.packages('ggplot2') # Install
library('ggplot2') # Load

Create an editable plot with ggplot2 :

library('ReporteRs')
library(ggplot2)
# Create a new powerpoint document
doc <- pptx()

# Add a new slide into the ppt document 
doc <- addSlide(doc, "Two Content" )

# add a slide title
doc<- addTitle(doc, "Editable vector graphics format versus raster format" )

# A function for creating a box plot
bp <- ggplot(data=PlantGrowth, aes(x=group, y=weight, fill=group))+
        geom_boxplot()

# Add an editable box plot
doc <- addPlot(doc, function() print(bp), vector.graphic = TRUE )

# Add a raster box plot
doc <- addPlot(doc, function() print(bp), vector.graphic = FALSE )

# write the document to a file
writeDoc(doc, file = "editable-ggplot2.pptx")

The PowerPoint document created by the R code above is available here : R software and ReporteRs package - create an editable ggplot2

Infos

This analysis has been performed using R (ver. 3.1.0).

You can read more about ReporteRs and download the source code at the following link :

GitHub (David Gohel): ReporteRs

Add a table into a Word document using R software and ReporteRs package

Sat, 09 Apr 2016 10:00:57 +0200

Add a simple table
Add a formatted table
Analyze, format and export a correlation matrix into a Word document
Powerpoint
Infos

The ReporteRs package is used to create a Word document from R software. The function addFlexTable() can be used to add a simple or customized table into the document.

The first step is to create a table using one of the functions below :

FlexTable() to create a ‘flexible’ table which can be easily formatted
vanilla.table() which is shortcut to quickly produce a nice FlexTable

The second step is to add the created table into the Word document using addFlexTable() function as follow :

# doc : docx object
# flextable : FlexTable object
addFlexTable(doc, flextable)

The aim of this R tutorial is to show you step by step, how to add simple and formatted table into a Word document.

In the following examples, we’ll add the first 5 rows of iris data sets into the Word document.

data<-iris[1:5, ]
data

  Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1          5.1         3.5          1.4         0.2  setosa
2          4.9         3.0          1.4         0.2  setosa
3          4.7         3.2          1.3         0.2  setosa
4          4.6         3.1          1.5         0.2  setosa
5          5.0         3.6          1.4         0.2  setosa

Add a simple table

library(ReporteRs)

doc <- docx()
data<-iris[1:5, ]

# Add a first table : Default table
doc <- addTitle(doc, "Default table")
doc <- addFlexTable( doc, FlexTable(data))

doc <- addParagraph(doc, c("", "")) # 2 line breaks

# Add a second table, theme : vanilla table
doc <- addTitle(doc, "Vanilla table")
doc <- addFlexTable( doc, vanilla.table(data))

writeDoc(doc, file = "r-reporters-word-document-add-table.docx")

An optional argument of addFlextable() function is par.properties which value can be parRight(), parLeft(), parJustify() for the table alignments. It can be used as follow :

doc <- addFlexTable( doc, vanilla.table(data),
                     par.properties = parCenter())

Note also that, row names are not shown by default when FlexTable() function is used to create a table. To make row names visible use the function as follow :

doc <- addFlexTable( doc, FlexTable(data, row.names=TRUE))

Add a formatted table

Change the background colors of rows and columns

You should know three functions to change the appearance of table rows and columns :

setZebraStyle() : to color odd and even rows differently; for example, odd rows in gray color and even rows in white color.
setRowsColors() : to change color of a particular table row
setColumnsColors : to change the color of particular table columns

These functions can be used as follow :

library(ReporteRs)

doc <- docx()

data<-iris[1:5, ]

# Zebra striped tables
doc <- addTitle(doc, "Zebra striped tables")
MyFTable <- vanilla.table(data)
MyFTable <- setZebraStyle(MyFTable, odd = '#eeeeee', even = 'white')
doc <- addFlexTable( doc, MyFTable)

# Change columns and rows background colors
doc <- addTitle(doc, "Change columns and rows background colors")
MyFTable = FlexTable(data = data )
# i : row index; j : column index
MyFTable = setRowsColors(MyFTable, i=2:3, colors = 'lightblue')
MyFTable = setColumnsColors(MyFTable, j=3, colors = 'pink' )
doc <- addFlexTable(doc, MyFTable)

writeDoc(doc, file = "r-reporters-word-document-formatted-table1.docx")

Note that, i and j are, respectively, the index of rows and column to change

Change cell background and text colors

We can change the background colors of some cells according to their values using the function setFlexTableBackgroundColors().

As an example, We’ll set up the background color of column 2 according to the value of the Sepal.Width variable (iris data sets) :

Cells with Sepal.Width < 3.2 are colored in gray (“#DDDDDD”)
Cells with Sepal.Width > = 3.2 are colored in “orange”

The text values of the table cells can be also customized as demonstrated in the example below :

library(ReporteRs)

doc <- docx()

data<-iris[1:5, ]

# Change the background colors of column 2 according to Sepal.Width
#++++++++++++++++++++++++++++
doc <- addTitle(doc, "Change the background color of cells")
MyFTable <- FlexTable(data)
MyFTable <- setFlexTableBackgroundColors(MyFTable, j = 2,
  colors = ifelse(data$Sepal.Width < 3.2, '#DDDDDD', 'orange'))

doc <- addFlexTable( doc, MyFTable)

# Format the text of some cells (column 3:4)
#++++++++++++++++++++++++++++
doc <- addTitle(doc, "Format cell text values")
MyFTable = FlexTable(data)
MyFTable[, 3:4] = textProperties(color = 'blue')
doc <- addFlexTable( doc, MyFTable)

writeDoc(doc, file = "r-reporters-word-document-format-cells.docx")

Insert content into a table : header and footer rows

Additional rows, such as header and footer, can be easily added into a table as illustrated in the example hereafter. Contents can be also added in a particular cell.

The functions addHeaderRow() and addFooterRow() are used to add a header and a footer.

A simplified format of these functions are :

addHeaderRow(x, value, colspan, text.properties)

addFooterRow(x, value, colspan, text.properties)

x : a FlexTable object
value : character vector to add as a header or a footer
colspan : a numeric vector (optional) specifying the number of columns to span for each corresponding value
text.properties : the text properties to apply to each cell (optional).

library(ReporteRs)
doc <- docx()

data<-iris[1:5, ]

# Insert a content into a table
doc <- addTitle(doc, "Insert a content")
MyFTable = FlexTable(data, header.columns= FALSE )

# Add first header row
MyFTable <- addHeaderRow( MyFTable, 
            value = c('Sepal', 'Petal', 'Species'), 
            text.properties = textBold(color="orange"), 
            colspan = c( 2, 2, 1))

# Add second header row
MyFTable = addHeaderRow(MyFTable, value = names(data),
  text.properties = textBold())
     
# Add footer row
MyFTable <- addFooterRow(MyFTable, 
              value = 'This data is from iris data sets',
              colspan = 5, 
              text.properties = textBoldItalic(color ="blue"))
# Add symbol
MyFTable[data$Petal.Length!=1.4, 'Species',
  text.properties = textBold(vertical.align = 'superscript',
                             color = "red")] = '(1)'
doc <- addFlexTable( doc, MyFTable)

writeDoc(doc, file = "r-reporters-word-document-add-header-footer.docx")

Analyze, format and export a correlation matrix into a Word document

library(ReporteRs)
doc <- docx()

data( mtcars )
cormatrix = cor(mtcars)

col =c("#B2182B", "#D6604D", "#F4A582", "#FDDBC7",
       "#D1E5F0", "#92C5DE", "#4393C3", "#2166AC")

mycut = cut(cormatrix,
        breaks = c(-1,-0.75,-0.5,-0.25,0,0.25,0.5,0.75,1),
        include.lowest = TRUE, label = FALSE )

color_palettes = col[mycut]

corrFT = FlexTable( round(cormatrix, 2), add.rownames = TRUE )

corrFT = setFlexTableBackgroundColors(corrFT,
        j = seq_len(ncol(cormatrix)) + 1,
        colors = color_palettes )


corrFT = setFlexTableBorders( corrFT
        , inner.vertical = borderProperties( style = "dashed", color = "white" )
        , inner.horizontal = borderProperties( style = "dashed", color = "white"  )
        , outer.vertical = borderProperties( width = 2, color = "white"  )
        , outer.horizontal = borderProperties( width = 2, color = "white"  )
)

doc <- addFlexTable( doc, corrFT)

writeDoc(doc, file = "r-reporters-word-document-correlation.docx")

Powerpoint

A pptx object works the same but does not require any parProperties

Infos

This analysis has been performed using R (ver. 3.2.3).

Saving Data into R Data Format: RDS and RDATA

Sat, 09 Apr 2016 09:25:52 +0200

Preleminary tasks
Save one object to a file
Save multiple objects to a file
Save your entire workspace
Summary
Related articles
Infos

In previous articles, we described the essentials of R programming and provided quick start guides for reading and writing txt and csv files using R base functions as well as using a most modern R package named readr, which is faster (X10) than R base functions. We also described different ways for reading and writing Excel files in R.

Writing data, in txt, csv or Excel file formats, is the best solution if you want to open these files with other analysis software, such as Excel. However this solution doesn’t preserve data structures, such as column data types (numeric, character or factor). In order to do that, the data should be written out in R data format.

Here, you’ll learn how to save i) a single R object, ii) multiple R objects or iii) your entire workspace in a specified file.

Saving data into R data formats can reduce considerably the size of large files by compression.

Preleminary tasks

Launch RStudio as described here: Running RStudio and setting up your working directory

Save one object to a file

It’s possible to use the function saveRDS() to write a single R object to a specified file (in rds file format). The object can be restored back using the function readRDS().

Note that, it’s possible to restore the object under a different name

The simplified syntax for saving and restoring is as follow:

# Save an object to a file
saveRDS(object, file = "my_data.rds")

# Restore the object
readRDS(file = "my_data.rds")

object: An R object to save
file: the name of the file where the R object is saved to or read from

In the R code below, we’ll save the mtcars data set and restore it under different name:

# Save a single object to a file
saveRDS(mtcars, "mtcars.rds")

# Restore it under a different name
my_data <- readRDS("mtcars.rds")

Save multiple objects to a file

The function save() can be used to save one or more R objects to a specified file (in .RData or .rda file formats). The function can be read back from the file using the function load().

Note that if you save your data with save(), it cannot be restored under different name. The original object names are automatically used.

# Saving on object in RData format
save(data1, file = "data.RData")

# Save multiple objects
save(data1, data2, file = "data.RData")

# To load the data again
load("data.RData")

Save your entire workspace

It’s a good idea to save your workspace image when your work sessions are long.

This can be done at any time using the function save.image()

save.image()

That stores your workspace to a file named .RData by default. This will ensure you don’t lose all your work in the event of system reboot, for instance.

When you close R/RStudio, it asks if you want to save your workspace. If you say yes, the next time you start R that workspace will be loaded. That saved file will be named .RData as well.

It’s also possible to specify the file name for saving your work space:

save.image(file = "my_work_space.RData")

To restore your workspace, type this:

load("my_work_space.RData")

Summary

Save and restore one single R object: saveRDS(object, file), my_data <- readRDS(file)
Save and restore multiple R objects: save(data1, data2, file = “my_data.RData”), load(“my_data.RData”)
Save and restore your entire workspace: save.image(file = “my_work_space.RData”), load(“my_work_space.RData”)

Infos

This analysis has been performed using R (ver. 3.2.3).

Writing Data From R to Excel Files (xls|xlsx)

Sat, 09 Apr 2016 08:27:41 +0200

Preleminary tasks
Writing Excel files using xlsx package
Summary
Related articles
Infos

Previously, we described the essentials of R programming and provided quick start guides for reading and writing txt and csv files using R base functions as well as using a most modern R package named readr, which is faster (X10) than R base functions. We also described different ways for reading data from Excel files into R.

Here, you’ll learn how to export data from R to Excel files (xls or xlsx file formats). We’ll use the xlsx R package.

Preleminary tasks

Launch RStudio as described here: Running RStudio and setting up your working directory

Writing Excel files using xlsx package

The xlsx package, a java-based solution, is one of the powerful R packages to read, write and format Excel files.

Installing and loading xlsx package

Install

install.packages("xlsx")

Load

library("xlsx")

Using xlsx package

There are two main functions in xlsx package for writing both xls and xlsx Excel files: write.xlsx() and write.xlsx2() [faster on big files compared to write.xlsx function].

The simplified formats are:

write.xlsx(x, file, sheetName = "Sheet1", 
  col.names = TRUE, row.names = TRUE, append = FALSE)

write.xlsx2(x, file, sheetName = "Sheet1",
  col.names = TRUE, row.names = TRUE, append = FALSE)

x: a data.frame to be written into the workbook
file: the path to the output file
sheetName: a character string to use for the sheet name.
col.names, row.names: a logical value specifying whether the column names/row names of x are to be written to the file
append: a logical value indicating if x should be appended to an existing file.

Example of usage: the following R code will write the R built-in data sets - USArrests, mtcars and iris - into the same Excel file:

library("xlsx")

# Write the first data set in a new workbook
write.xlsx(USArrests, file = "myworkbook.xlsx",
      sheetName = "USA-ARRESTS", append = FALSE)

# Add a second data set in a new worksheet
write.xlsx(mtcars, file = "myworkbook.xlsx", 
           sheetName="MTCARS", append=TRUE)

# Add a third data set
write.xlsx(iris, file = "myworkbook.xlsx",
           sheetName="IRIS", append=TRUE)

Read more about for reading, writing and formatting Excel files:

Summary

Write data from R to Excel files using xlsx package: write.xlsx(my_data, file = “result.xlsx”, sheetName = “my_data”, append = FALSE).

Infos

This analysis has been performed using R (ver. 3.2.3).

Fast Writing of Data From R to txt|csv Files: readr package

Sat, 09 Apr 2016 08:18:39 +0200

Preleminary tasks
Installing and loading readr
readr functions for writing data
Writing data to a file
Summary
Related articles
Infos

There are many solutions for writing data from R to txt (i.e., tsv: tab-separated values) or csv (comma-separated values) files. In our previous articles, we described R base functions (write.table() and write.csv()) for writing data from R to txt|csv files R.

In this article, we’ll describe a most modern R package readr, developed by Hadley Wickham, for fast reading and writing delimited files. It contains the function write_delim(), write_csv() and write_tsv() to export easily a data from R.

Compared to R base functions (write.csv() and write.table()), readr functions:

are much faster (X2),
never write row names.

Preleminary tasks

Launch RStudio as described here: Running RStudio and setting up your working directory

Installing and loading readr

# Installing
install.packages("readr")

# Loading
library("readr")

readr functions for writing data

The function rwrite_delim()[in readr package] is a general function to export a data table from R. Depending on the format of your file, you can also use:

write_csv(): to write a comma (“,”) separated values
write_tsv(): to write a tab separated (“\t”) values

The simplified format of these functions are, as follow:

# General function
write_delim(x, path, delim = " ")

# Write comma (",") separated value files
write_csv(file, path)

# Write tab ("\t") separated value files
write_tsv(file, path)

x: a data frame to be written
path: path to the result file
delim: Delimiter used to separate values. Must be single character.

Writing data to a file

The R code below exports the built-in R mtcars data set to a tab-separated ( sep = “\t”) file called mtcars.txt in the current working directory:

# Loading mtcars data
data("mtcars")


library("readr")
# Writing mtcars data to a tsv file
write_tsv(mtcars, path = "mtcars.txt")

# Writing mtcars data to a csv file
write_csv(mtcars, path = "mtcars.csv")

Summary

Write data from R to a txt (i.e., tsv) file: write_tsv(my_data, path = “my_data.txt”)
Write data from R to a csv file: write_csv(my_data, path = “my_data.csv”)

Infos

This analysis has been performed using R (ver. 3.2.3).

Writing Data From R to txt|csv Files: R Base Functions

Sat, 09 Apr 2016 08:11:48 +0200

Preleminary tasks
R base functions for writing data
Writing data to a file
Summary
Related articles
Infos

Previously, we described R base functions (read.delim() and read.csv()) for importing txt and csv files into R.

In this article, you’ll learn how to export or write data from R to .txt (tab-separated values) and .csv (comma-separated values) file formats.

Preleminary tasks

Launch RStudio as described here: Running RStudio and setting up your working directory

R base functions for writing data

The R base function write.table() can be used to export a data frame or a matrix to a file.

A simplified format is as follow:

write.table(x, file, append = FALSE, sep = " ", dec = ".",
            row.names = TRUE, col.names = TRUE)

x: a matrix or a data frame to be written.
file: a character specifying the name of the result file.
sep: the field separator string, e.g., sep = “\t” (for tab-separated value).
dec: the string to be used as decimal separator. Default is “.”
row.names: either a logical value indicating whether the row names of x are to be written along with x, or a character vector of row names to be written.
col.names: either a logical value indicating whether the column names of x are to be written along with x, or a character vector of column names to be written. If col.names = NA and row.names = TRUE a blank column name is added, which is the convention used for CSV files to be read by spreadsheets.

It’s also possible to write csv files using the functions write.csv() and write.csv2().

write.csv() uses “.” for the decimal point and a comma (“,”) for the separator.
write.csv2() uses a comma (“,”) for the decimal point and a semicolon (“;”) for the separator.

The syntax is as follow:

write.csv(my_data, file = "my_data.csv")

write.csv2(my_data, file = "my_data.csv")

Writing data to a file

The R code below exports the built-in R mtcars data set to a tab-separated ( sep = “\t”) file called mtcars.txt in the current working directory:

# Loading mtcars data
data("mtcars")

# Writing mtcars data
write.table(mtcars, file = "mtcars.txt", sep = "\t",
            row.names = TRUE, col.names = NA)

If you don’t want to write row names, use row.names = FALSE as follow:

write.table(mtcars, file = "mtcars.txt", sep = "\t",
            row.names = FALSE)

Summary

Write data from R to a txt file: write.table(my_data, file = “my_data.txt”, sep = “”)
Write data from R to a csv file: write.csv(my_data, file = “my_data.csv”)

Infos

This analysis has been performed using R (ver. 3.2.3).

Create a Word document from a template file using R software and ReporteRs package

Sun, 04 Jan 2015 01:02:07 +0100

Quick introduction to ReporteRs package
Create a Word document using a template file
Infos

This tutorial describes how to create a Word document based on an existing one using R software and Reporters package. In this case, your final Word document is generated using the layout and the styles from the template file.

This approach is useful in many situations :

If you work in a corporate environment, you may need sometimes to generate Word documents based on a template with specific fonts, color, logos, etc.
If you want to insert R outputs in an existing Word document.
If you want to use text formatting styles from a given template file.

Before reading this article you should take a look at my first post : Create and format Word documents using R software and Reporters package.

Quick introduction to ReporteRs package

ReporteRs package provides simple functions to quickly generate and format a word document from R software. It can be used as follow :

#install.packages("ReporteRs")
library("ReporteRs")

# Create a Word document
doc <- docx()

# Add a title
doc <- addTitle(doc, "Example of a Word document from R software", level=1)

# Add paragraph
doc <- addParagraph(doc, "This Word document has been generated from R software using ReporteRs package.")

# Add plots
doc <- addTitle(doc, "Plots", level=1)
doc <- addPlot(doc, function() hist(iris$Sepal.Width, col=4) )

doc <- addPageBreak(doc) # go to the next page

# Add table
doc <- addTitle(doc, "Table", level=1)
doc <- addFlexTable(doc, vanilla.table(iris[1:10,]))

# Write the word document to a file
writeDoc(doc, file="r-reporters-word-example.docx")

The Word document created by the R code above is available here : R software and ReporteRs package - Example of a Word document

Create a Word document using a template file

A template file can be specified to the docx() function as follow :

# Create a word document
doc <- docx(template="path/to/your/word/template/file.docx")

# ...............
# Add contents
# ...............

# Write the Word document to a file 
writeDoc(doc, file = "output-file.docx")

In the R code below, a Word document template is downloaded from STHDA website and used to write a report :

# Download a Word document template from STHDA website
download.file(url="https://www.sthda.com/sthda/RDoc/example-files/r-reporters-word-document-template.docx",
    destfile="r-reporters-word-document-template.docx", quiet=TRUE)

# Create a Word document using the downloaded template
doc <- docx(title="R software and ReporteRs package",
            template="r-reporters-word-document-template.docx")

# Add titles
doc <- addTitle(doc, "Word document created from a template",
                level=1) 

# Add an introduction
doc <- addTitle(doc, "Introduction", level=2) # Add a sub title
doc <- addParagraph(doc, "This Word document is created from a template using R software and ReporteRs package.")

# Add  a table
doc <- addTitle(doc, "Iris data sets", level=2)
doc <- addFlexTable(doc, FlexTable(iris[1:10,]))
doc <- addTitle(doc, "Description of iris data sets", level=2)
doc <- addParagraph(doc, "iris data set gives the measurements in centimeters of the variables sepal length and width and petal length and width, respectively, for 50 flowers from each of 3 species of iris. The species are Iris setosa, versicolor, and virginica.")

# Add a page break : go to next page
doc <- addPageBreak(doc)

# Add a plot into the Word document
doc <- addTitle(doc, "Nice bar plot")
doc <- addPlot(doc, function() barplot(1:5, col=1:5))

# Write the Word document to a file 
writeDoc(doc, file = "r-reporters-word-document-from-template.docx")

# Remove the downloaded template file
ok <- file.remove("r-reporters-word-document-template.docx")

The Word document created by the R code above is available here : R software and ReporteRs package - Word document created from a template

Note that, the function docx() can take two arguments : a title argument (title of the document, appearing only in the Word document properties) and a template argument (to specify template file).

Infos

This analysis has been performed using R (ver. 3.1.0).

You can read more about ReporteRs and download the source code at the following link :

GitHub (David Gohel): ReporteRs

Create and format Word documents using R software and Reporters package

Sat, 03 Jan 2015 22:52:48 +0100

Install and load the ReporteRs R package
Create a simple Word document
Add a table of contents into a Word document
Infos

Word document is one of the file formats widely used by many people, including researchers, for editing their text and tracking changes between different authors.

There are different solutions to generate a Word document from R software :

R2wd package : unfortunately it depends on statconnDCOM or RDCOMClient servers, and works on Windows only.
knitr + rmarkdown + pandoc : this is an easy way to quickly create a Word report but the output is very basic.
ReporteRs package, by David Gohel, provides easy to use functions to write and format Word documents. It can be also used to generate Word document from a template file with logos, fonts, etc. ReporteRs is Java-based solution, so it works on Windows, Linux and Mac OS systems.

The aim of this R tutorial is to show you how to easily and quickly export outputs (including data table, plots, paragraphs of text and R scripts) from R statistical software to a Microsoft Word document (.docx file format) using ReporteRs package.

Install and load the ReporteRs R package

ReporteRs can be installed and loaded as follow :

install.packages('ReporteRs') # Install
library('ReporteRs') # Load

Note that ReporteRs requires Java (>= 1.6) ; make sure you have an installed JRE

The version of Java installed on your computer, can be checked with this R code :

system("java -version")

Create a simple Word document

Word document can be created using the docx() function. Then, contents can be added to the document using the functions below:

addTitle: Add a title
addParagraph: Add paragraphs of text
addFlexTable: Add a table
addPlot: Add a plot generated in R
addImage: Add external images
addTOC: Add a table of contents
addRScript: highlight and add R code
addMarkdown: Add markdown
addPageBreak: Add a page break

After adding contents, you have to use the writeDoc() function to write the Word document into a .docx file.

Add texts : title and paragraphs of texts

Texts can be added as a title or a paragraph using the R functions addTitle() or addParagraph(). A simplified format of these functions are :

addTitle(doc, value, level=1) # Add titles
addParagraph(doc, value) # Add a paragraph of texts

doc : docx object.
value : the text to add as a title or a paragraph.
level : an integer specifying the heading level. e.g : 1 for title1, 2 for title2, 3 for title3, etc.

addTitle() and addParagraph() functions can be used as follow :

library(ReporteRs)

# Create a word document to contain R outputs
doc <- docx()

# Add a title to the document
doc <- addTitle(doc, "Simple Word document", level=1)

# Add a paragraph of text into the Word document 
doc <- addParagraph(doc, "This simple Word document is created using R software and ReporteRs package. It contains just a simple text.")

# Add a sub title
doc <- addTitle(doc, "What is R language?", level = 2) 
doc <- addParagraph(doc, "R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical and graphical techniques, and is highly extensible.")

doc <- addTitle(doc, "What is ReporteRs", level = 2)
doc <- addParagraph(doc, "ReporteRs is a package to write and format easily a Word document from R software.")

# Write the Word document to a file 
writeDoc(doc, file = "r-reporters-simple-word-document.docx")

Format the text of a Word document using R software

Text properties : font, color, size

Among the text properties available in a Word document, there are :

font family (e.g : “Arial”), font size (e.g : 11), font weight (e.g: bold), font style (e.g : italic), underlined text, vertical align (superscript, subscript) and color (e.g: “blue”).

These properties are shown in the figure below :

This section describes how to format and write a Word document using R software

Change the global font size and font family

The default font size and font family can be changed as follow :

options( "ReporteRs-fontsize" = 12, 
         "ReporteRs-default-font" = "Arial")

Note that, this changing will be applied to the whole content of the Word document. An example is shown in the next section.

Change the appearance of a “Piece Of Text” (pot)

The function pot() [Pieces Of Text] is used to format text chunks before adding into the document. pot() function can be also used to create a hyperlink and a footnote. A simplified format is :

pot(value="", format = textProperties())

value : the text to be formatted
format : the properties to use for formatting the text

The possible values for the parameter format are the following functions :

textProperties() : the text formatting properties
textBold() : shortcut for bold text
textItalic() : shortcut for italic text
textBoldItalic() : shortcut for bold-italic text
textNormal() : shortcut for normal text

The arguments for these functions are :

color : font color; e.g : color=“#000000” or color = “black”.
font.size : a integer indicating the font size.
font.weight : the font weight. Possible values are “normal” or “bold”.
font.style : the font style. Possible values are “normal” or “italic”.
underlined : a logical value specifying if the text should be underlined.
font.family : the font family; e.g : “Arial”.
vertical.align : a character indicating font vertical alignments. Expected values are “baseline”" or “subscript” or “superscript”. Default value is baseline.
shading.color : background color of the text (e.g “#000000” or “black”)

pot() function can be used as follow :

# Formatted text
my_text <- 'This is a ' + 
         pot('formatted text', textProperties(color="blue")) + 
        ' created using' + pot('ReporteRs', textBold()) + 'package'

# Create a hyperlynk
my_link <- pot( 'Click here to visit STHDA website!', 
          hyperlink = 'https://www.sthda.com/english',
          format=textBoldItalic(color = '#428BCA', underline = TRUE ))

The R code below creates a Word document containing a formatted text and a hyperlink :

doc <- docx() 

# Change the default font size and font family
options('ReporteRs-fontsize'=12, 'ReporteRs-default-font'='Arial')

# Add a formatted paragraph of texts
#++++++++++++++++++++++++++++++
doc <- addTitle(doc, "Formatted text", level=1)
# Define a style to highlight a text
highlight_style <- textProperties(color='#1163A5',font.size = 20,
                font.weight = 'bold', font.family = 'Courier New' )

my_text = 'This ' + pot('Word document', highlight_style) +
  ' is created using' +
  pot(' R software', textProperties(color="red", font.size=18)) +
  ' and'+
  pot(' ReporteRs', textBoldItalic(color="#F0A91B", underlined=TRUE)) + ' package.'
doc <- addParagraph(doc, my_text)

# Add a hyperlink
doc <- addTitle(doc, "STHDA Web site", level=1)
my_link <- pot('Click here to visit STHDA web site!', 
          hyperlink = 'https://www.sthda.com/english',
          format=textBoldItalic(color = 'blue', underline = TRUE ))
doc <- addParagraph(doc, my_link)

# Write the Word document to a file 
writeDoc(doc, file = "r-reporters-formatted-word-document.docx")

Add plots and images

The functions addPlot() and addImage() can be used for adding a plot or an external image to the document. addPlot() works with all R plots (base graphics, lattice, ggplot2 and grid).

The format of these 2 functions are :

# Add plots
# fun : R plotting function
# ... : other arguments to pass to the plotting function
addPlot(doc, fun, ...)

# Add images
# filename : path to the external image
addImage(doc, filename)

The R code below creates a Word document containing an introduction, a box plot, a histogram and an image (downloaded from STHDA web site).

doc <- docx() # Create a Word document

# Add a title
doc <- addTitle(doc, "Word document with plots and Images", 
                level = 1)

# Add an introduction
doc <- addTitle(doc, "Introduction", level = 2)
doc = addParagraph(doc, value ="This Word document is created using R software and ReporteRs package. The goal of this section is to show you how to add plots and images into a Word document. This can be done easily using the functions addPlot() and addImages().")

# Add a box plot
doc <- addTitle(doc, "Box plot using R software", level = 2)
boxplotFunc<-function(){
  boxplot(len ~ dose, data = ToothGrowth,
      col = rainbow(3), main = "Guinea Pigs' Tooth Growth",
      xlab = "Vitamin C dose mg", ylab = "tooth length")
}
doc <- addPlot(doc, boxplotFunc)
 
doc <- addPageBreak(doc) # Go to the next page

# Add a histogram
doc <- addTitle(doc, "Histogram plot", level = 2)
doc <- addPlot(doc, function() hist(iris$Sepal.Width, col="lightblue"))

# Change point size of plotted text (in pixels, default = 12)
doc <- addTitle(doc, "Histogram with pointsize = 18", level = 2)
doc <- addPlot(doc, function() hist(iris$Sepal.Width,col="lightblue"), pointsize=18)

# Add an image
# +++++++++++++++++++++++++++
# download an image from STHDA web site
download.file(url="https://www.sthda.com/sthda/RDoc/figure/easy-ggplot2/ggplot2-histogram-demo.png",
              destfile="ggplot2-histogram-demo.png", quiet=TRUE)

doc <- addTitle(doc, "Image from STHDA web site", level = 2)
doc <- addImage(doc, "ggplot2-histogram-demo.png")

# Write the Word document to a file 
writeDoc(doc, file = "r-reporters-word-document-with-plot.docx")

The Word document created by the R code above is available here : R software and ReporteRs package - Word document containing plots

Note that, for addPlot() function, you can use the arguments width and height to specify the plot width and height in inches (default values are 6 X 6)
Another optional argument of addPlot() function is par.properties which value can be parRight(), parLeft(), parJustify() for the plot alignments:

doc <- addPlot( doc = doc, fun = function(){
    barplot( 1:5, par.properties = parCenter() )} 
  )

For addImage() function, the allowed file formats are PNG, WMF, JPEG and GIF images..

Add a table

The function addFlexTable() is used to add a simple or customized table.

The first step is to create a table using one of the functions below :

FlexTable() to create a ‘flexible’ table which can be easily formatted
vanilla.table() which is shortcut to quickly produce a nice FlexTable

The second step is to add the created table into the Word document using addFlexTable() function as follow :

# doc : docx object
# flextable : FlexTable object
addFlexTable(doc, flextable)

Add a simple table

doc <- docx()
data<-iris[1:5, ]

# Add a first table : Default table
doc <- addTitle(doc, "Default table")
doc <- addFlexTable( doc, FlexTable(data))

doc <- addParagraph(doc, c("", "")) # 2 line breaks

# Add a second table, theme : vanilla table
doc <- addTitle(doc, "Vanilla table")
doc <- addFlexTable( doc, vanilla.table(data))

writeDoc(doc, file = "r-reporters-word-document-add-table.docx")

Add a zebra striped table

setZebraStyle() function can be used to color odd and even rows differently; for example, odd rows in gray color and even rows in white color.

doc <- docx()

data<-iris[1:5, ]

# Zebra striped tables
doc <- addTitle(doc, "Zebra striped tables")
MyFTable <- vanilla.table(data)
MyFTable <- setZebraStyle(MyFTable, odd = '#eeeeee', even = 'white')
doc <- addFlexTable( doc, MyFTable)

writeDoc(doc, file = "r-reporters-word-document-zebra.docx")

Add lists : ordered and unordered lists

Ordered and unordered lists can be added using addParagraph() function as follow :

doc = addParagraph(doc, 
  value = c('Item 1', "Item 2", "Item 3")
  par.properties = parProperties(list.style = 'ordered', level = 1 )

value : a set of texts to be added as a list
par.properties : the paragraph formatting properties
- list.style : possible values are ‘unordered’ and ‘ordered’
- level : a numeric value indicating the level of the item to be added in the list

Add simple lists

doc <- docx()

# Ordered list
doc <- addTitle(doc, "Ordered List")
doc <- addParagraph(doc, value= c("Item 1", "Item 2", "Item 3"),
          par.properties =  parProperties(list.style = 'ordered'))

# Unordered list
doc <- addTitle(doc, "Unordered List")
doc <- addParagraph(doc, value= c("Item 1", "Item 2", "Item 3"),
          par.properties =  parProperties(list.style = 'unordered'))

writeDoc(doc, file = "r-reporters-word-document-lists.docx")

Add multi-level lists

To simplify the code, we’ll first define some levels to be used for creating multi-level lists.

doc <- docx()

# Define some levels for ordered lists (ol)
ol1 = parProperties(list.style = "ordered", level = 1)
ol2 = parProperties(list.style = "ordered", level = 2)

# Define some levels for unordered lists (ul)
ul1 = parProperties(list.style = "unordered", level = 1)
ul2 = parProperties(list.style = "unordered", level = 2)

# Multi-lvel ordered list
doc <- addTitle(doc, "Ordered List")
doc <- addParagraph(doc, value= "Item 1", par.properties =  ol1)
doc <- addParagraph(doc, value= "Item 1.1", par.properties =  ol2)
doc <- addParagraph(doc, value= "Item 1.2", par.properties =  ol2)
doc <- addParagraph(doc, value= "Item 2", par.properties =  ol1)


# Multi-lvel unordered list
doc <- addTitle(doc, "Unordered List")
doc <- addParagraph(doc, value= "Item 1", par.properties =  ul1)
doc <- addParagraph(doc, value= "Item 1.1", par.properties =  ul2)
doc <- addParagraph(doc, value= "Item 1.2", par.properties =  ul2)
doc <- addParagraph(doc, value= "Item 2", par.properties =  ul1)

writeDoc(doc, file = "r-reporters-word-document-multilevel-lists.docx")

Add a footnote to a Word document

A footnote is a set of paragraphs written at the bottom of the Word document.

The steps for adding a footnote into a document are :

Create a footnote object using the function Footnote()
Add a text to the footnote using the function addParagraph()

library(ReporteRs)

doc <- docx()

# create footnotes
footnote1 <- Footnote( ) # footnote1 about R
footnote1 <- addParagraph(footnote1, "R is a free software for statistical computing and graphics.")

footnote2 <- Footnote( ) # footnote2 about ReporteRs package
footnote2 <- addParagraph(footnote2, "ReporteRs is an R package to write and format easily a Word document.")

# Use the footnotes when writing a paragraph into the document
doc <- addTitle(doc, "Word document with a footnote", level=1)
doc <- addParagraph(doc, 
      "This Word document is created using " + 
      pot("R software", footnote=footnote1)+ " and "+
      pot("ReporteRs", footnote=footnote2) +" package."
      )

writeDoc(doc, file = "r-reporters-word-document-footnote.docx")

Add R scripts

The function addRScript() can be used as follow :

doc <- docx()

r_code <- 'summary(cars$dist)
x <- rnorm(100)
hist(x)
'

# Change the backgroud-color
doc <- addRScript(doc, text = r_code,
    par.properties= parProperties(shading.color = 'gray90'))

writeDoc(doc, file = "r-reporters-word-add-r-code.docx")

Add a table of contents into a Word document

To add a table of contents, the function addTOC() can be used.

Note that, when a table of content (TOC) is added into a Word document, a message box is displayed when opening the file for the first time. This message asks if you want to update TOC entries. This is not an error and you should click ‘Yes’ to update TOC entries. You should save the document to avoid this to happen the next time.

doc <- docx() # Create a Word document

# Add a title
doc <- addTitle(doc, "Create a Word document with TOC", level = 1)

# Add a table of contents
doc <- addTOC(doc)

doc <- addPageBreak(doc) # go to the next page

# Add an introduction
doc <- addTitle(doc, "Introduction", level = 2)
doc = addParagraph(doc, value ="This Word document is created using R software and ReporteRs package. The goal of this section is to show you how to add a table of contents into a Word document. This can be done easily using the function addTOC.")

# Add a box plot
doc <- addTitle(doc, "Box plot using R software", level = 2)
boxplotFunc<-function(){
  boxplot(len ~ dose, data = ToothGrowth,
      col = rainbow(3), main = "Guinea Pigs' Tooth Growth",
      xlab = "Vitamin C dose mg", ylab = "tooth length")
}
doc <- addPlot(doc, boxplotFunc)
 
doc <- addPageBreak(doc) # go to the next page

# Add plots
#+++++++++++++++++++++
doc <- addTitle(doc, "Basic plots using R software", level = 2)
doc <- addParagraph(doc, "R is a free software for plotting and data analysis. This chapter contains examples of graphs generated using R.")

# Add a histogram
doc <- addTitle(doc, "Histogram", level = 3)
doc <- addPlot(doc, function() hist(iris$Sepal.Width,
                                  col="lightblue"))

doc <- addPageBreak(doc) # go to the next page

# Add a bar plot
doc <- addTitle(doc, "Bar plot", level = 3)
doc <- addPlot(doc, function() barplot(VADeaths))

# Write the Word document to a file 
writeDoc(doc, file = "r-reporters-word-document-toc.docx")

The Word document created by the R code above is available here : R software and ReporteRs package - Word document with a table of contents

Infos

This analysis has been performed using R (ver. 3.1.0).

You can read more about ReporteRs and download the source code at the following link :

GitHub (David Gohel): ReporteRs

Easy Guides

Exporting Data From R

Create and format PowerPoint documents from R software

Why is it important to be able to generate a PowerPoint report from R ?

Reason I : Many collaborators works with Microsoft office tools

Reason II : keeping beautiful R graphs beautifull for publications

But wasn’t this problem solved already?

Objective

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Slide layout

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Powerpoint

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