Last articles - STHDA : R

R2DOCX : Create a word document with R

Fri, 19 Jul 2013 01:04:01 +0200

Two ways to generate a word document. Either with Knitr and pandoc or with R2DOCX.

Pandoc : Convert Markdown documents to other formats

For more information click here

The pandoc() function is included in the knitr package (version 1.2) and it could be used to convert Markdown documents to other formats such as Latex/PDF, HTML and Word (. Doc,. Docx).

To install pandoc click-here

How to use pandoc()

Code R :

 
library(knitr)
pandoc('foo.md', format='html')  # HTML
pandoc('foo.md', format='latex') # LaTeX/PDF
pandoc('foo.md', format='docx')  # MS Word
pandoc('foo.md', format='odt')   # OpenDocument

Create a Word document with R2DOCX

Using R2DOCX package you can, create easly a Word document from a template or not and add a plot or table to the document.

A comprehensive documentation is available here
An example is shown here

Installation

Compatibility R >= 3.0

Code R :

 
install.packages("devtools")
devtools::install_github('R2DOC', 'davidgohel')
devtools::install_github('R2DOCX', 'davidgohel')

For Mac users :

Code R :

 
Sys.setenv(NOAWT=1) #prevents usage of awt.[http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Java-_0028OS-X_0029]
install.packages("devtools")
devtools::install_github('R2DOC', 'davidgohel')
devtools::install_github('R2DOCX', 'davidgohel')

The available functions

addPlot for adding plots.
addParagraph for adding paragraphs of text.
addTable for adding tables.
addHeader for adding headers.
addTOC for adding tables of contents.
addPageBreak for adding a page break.
addLineBreak for adding a line break.
replaceText for text replacement.

Your first document

Code R :

 
Sys.setenv(NOAWT=1) #prevents usage of awt - required on Mac
library(R2DOCX)
 
# The file to create
docx.file <- "document.docx"
# Docx object to manipulate
doc <- new ("Docx", title = "My example" )
#Add a table
doc = addTable( doc, iris[1:10,] )
# Add atext
doc <- addParagraph( doc, value = "Hello World!", stylename = "Normal" )
# Add a plot
doc = addPlot( doc, function() plot( rnorm(10), rnorm(10) )
               , width = 10, height = 8
)
# Write the file
writeDoc( doc, docx.file )

Create a Word document from template

Code R :

 
# Document to create
docx.file = "document.docx"
# Word document used as template
template.file = file.path( find.package("R2DOCX"), "templates/TEMPLATE_01.docx", fsep = "/" )
# Create an object
doc = new("Docx"
	, title = "My example" 
	, basefile = template.file
)
# 2 keywords exist in the base file- Let's replace it
doc = replaceText( doc, pattern = "AUTHOR", replacement = "John Doe" )
doc = replaceText( doc, pattern = "DATE", replacement = date() )

Main title

Code R :

 
#Main title
#**************************************
doc = addParagraph( doc, value = "Exemple", stylename = "TitleDoc" )
doc = addPageBreak( doc ) #saut de page

Code R :

 
#Table of content : TOC
#**************************************
#(user will be asked to update this TOC  when document will be opened the first time)
doc = addHeader(doc, "Table des matières", 1);
doc = addTOC(doc)
doc = addPageBreak( doc )#saut de page

Add texts (Normal et list)

Code R :

 
# Add texts (Normal et list)
#**************************************
doc = addHeader(doc, "Dataset presentation", 1);
#Normal style
doc = addParagraph( doc, value = "Dataset 'measured.weights' is set of weights measurements collected on few people before savate training.", stylename = "Normal" )
#Unordered list
texts = c( "Column 'gender' is the subject gender." 
           , "Column 'id' is the unique subject identifier." 
           , "Column 'cat' is the subject weight category." 
           , "Column 'competitor' tells wether or not subject practice competition." 
           , "Column 'day' is the day of measurement." 
           , "Column 'weight' is the measured weight." 
)
doc = addParagraph( doc, value = texts, stylename = "BulletList" )

Conditionnal formating of the text

The addParagraph function is used to simply add text as shown above. It can also be used to replace text and to make conditional formatting in the document.

Code R :

 
# template text
x = "[animal] eats [food]."
# define formatting properties for replacement text – see chapter "styles"
textProp = textProperties( color = "blue" )
replacement.styles = list( animal= textProp, food= textProp )
# define replacement text
replacements = list( animal = "donkey", food = "grass" )
 
doc <- addParagraph( doc, value = x, stylename = "Normal"
                     , replacements = replacements
                     , replacement.styles = replacement.styles
)

textProperties function

Code R :

textProperties(color = "black", font.size = 10
		, font.weight = "normal", font.style = "normal"
		, font.family = "Arial" )

color : font color; font.size: size in pixel; font.weight : "normal" ou "bold"; font.style: "normal" ou "italic"; font.family: font family.

Add a table

Simple table:

Code R :

 
# Add a table
#**************************************
# Used data
data( measured.weights )
doc = addHeader(doc, "Dataset", 1);
doc = addHeader(doc, "Dataset first lines", 2);
#Simple table
doc = addTable( doc
                , data = head( measured.weights, n = 10 )
                , formats = get.light.formats()
)
doc = addLineBreak( doc )#Line break

Rename table headers:

Before you rename:

Code R :

 
doc = addTable( doc, data = weights.summary)

After you rename :

Code R :

 
doc = addTable( doc
		, data = weights.summary
		, header.labels = list("id" = "Subject Identifier", "avg.weight" = "Average Weight"
				, "regularity" = "Regularity", "visit.n" = "Number of visits", "last.day" = "Last visit"
				) # columns labels to display
		)

Simple table customized with merged rows :

In the table below, the rows are merged on the 'day' column. The column 'gender' is colored by gender.

Code R :

 
# simple addTable with row merging on 'day' column
doc = addHeader(doc, "Dataset last lines", 2);
sampledata = tail( measured.weights[ order(measured.weights$day), ], n = 20 )
doc = addTable( doc
		, data = sampledata
		, span.columns = c("day")
		, col.colors = list( "gender" = ifelse( sampledata$gender == "male" , "#00c2ff", "#ffcdd1") )
)

Customized table with grouped headers:

In this table, headers have been renamed, grouped headers are created, the type of columns is specified (%, integre, character, decimal, date). The values of the "Regularity" column were colored according to the value (gray if <0.5 and blue if> = 0.5).

Code R :

 
# customized table
doc = addHeader(doc, "Dataset summary", 1);
doc = addTable( doc
		, data = weights.summary
		, header.labels = list("id" = "Subject Identifier", "avg.weight" = "Average Weight"
				, "regularity" = "Regularity", "visit.n" = "Number of visits", "last.day" = "Last visit"
				) # columns labels to display
		, grouped.cols=list( "id" = "id"
				, "Summary" = c( "avg.weight",  "regularity", "visit.n", "last.day" ) 
				) # grouped headers line to add before headers line
		, col.types = list( "id" = "character", "avg.weight" = "double"
				, "regularity" = "percent", "visit.n" = "integer"
				, "last.day" = "date" ) # reporting types of each columns 
		, col.fontcolors = list( "regularity" = ifelse( weights.summary$regularity < 0.5 , "gray", "blue") ) # customized font colors for column "regularity"
)

Add a plot

Code R :

 
# Add a plot
#**************************************
doc = addPageBreak( doc )
doc = addHeader(doc, "Graphics", 1);
doc = addPlot( doc,
               function() boxplot(measured.weights$weight ~ measured.weights$id,
                                  xlab = "Subjects", ylab = "Weights" , col = "#0088cc",
                                  legend = "My boxplot"),
               width=7, height=7
              )

Text replacement

To replace the keyword "AUTHOR" ,in the word document, with "Pearson":

Code R :

 
doc = replaceText( doc, "AUTHOR", "Pearson")

Heading styles available in your document

Code R :

 
doc <- new("Docx", title = "My example" )
styles( doc )
# [1] "Normal"                  "Titre1"                  "Titre2"                 
# [4] "Titre3"                  "Titre4"                  "Titre5"                 
# [7] "Titre6"                  "Titre7"                  "Titre8"                 
#[10] "Titre9"                  "Policepardfaut"          "TableauNormal"          
# ...
doc <- setHeaderStyle(doc, stylenames = c("Titre1", "Titre2", "Titre3", "Titre4", "Titre5", "Titre6", "Titre7", "Titre8", "Titre9" ) ) 
doc = addHeader( doc, "title 1", 1 )

A full word document

The full script used to create this word document can be downloaded here: R2DOCX.r

A full word document

Create an animated .gif image with R and ImageMagick

Thu, 09 Aug 2012 21:10:01 +0200

The purpose of this tutorial is to show you the steps to create an animated gif image with R and ImageMagick. You must first install ImageMagick.

It is also possible to create animated .gif images using only R, through write.gif() in caTools package.

The R code described in this tutotriel were tested on Mac OS X 10.6.8 with R 2.13

Example 1: Create a countdown

R code

The countdown is from 10 to 1. We will create it in 4 steps.

1 - Creating a clean working directory called 'examples'.
2 - Creating .png images, each containing a number (10 to 1).
3 - Creating a single image. Gif using ImageMagick
4 - delete png files that are no longer needed

The corresponding R code is shown below:

Code R :

 
#crearing working directory
dir.create("examples")
setwd("examples") 
 
#Creating countdown .png files from 10 to "GO!"
png(file="example%02d.png", width=200, height=200)
  for (i in c(10:1, "G0!")){
    plot.new()
    text(.5, .5, i, cex = 6)
  }
dev.off()
 
# Converting .png files in one .gif image using ImageMagick
system("/opt/local/bin/convert -delay 80 *.png example_1.gif")
# Remove .png files from working directory
file.remove(list.files(pattern=".png"))

1 - The system() function executs the conversion command as in a terminal. I use the absolute path to the convert command. In my case it is: /opt/ local/bin/convert. In some cases the command system("convert -delay 80 *. Example_1.gif png") works.

2 - the flag -delay is the time between two images (the speed of the animation).
3-The part "%02d" in the filename increment automatically the .png file names

Result

The result is :

Example 2: Creating a 3D animated graphic

We will create a 3D surface plot to visualize a linear model using lattice package. 3D graphics can be created also with rgl package.

R code

Code R :

 
library(lattice)
b0 <- 10
b1 <- .5
b2 <- .3
g <- expand.grid(x = 1:20, y = 1:20)
g$z <- b0 + b1*g$x + b2*g$y
 
png(file="example%03d.png", width=300, heigh=300)
  for (i in seq(0, 350 , 10)){
    print(wireframe(z ~ x * y, data = g,
              screen = list(z = i, x = -60)))
  }
dev.off()
 
# converting .png file in .gif using ImageMagick
system("/opt/local/bin/convert -delay 40 *.png example_2_reduced.gif")
 
# Remove .png file
file.remove(list.files(pattern=".png"))

Result

Source :
http://ryouready.wordpress.com/2010/11/21/animate-gif-images-in-r-imagemagick/

Loading data in R from internet

Sat, 04 Aug 2012 18:33:01 +0200

Importing a *. txt file from the Internet

Import decathlon.txt file from STHDA web site: :

Code R :

 
data=read.table(file="https://www.sthda.com/upload/decathlon.txt", 
                       header=T, row.names=1, sep="\t") #Importation des données
print(data) # Print the data

Load .rdata file from internet

To do this, you must first create a connection using the R url function. You can then load the connexion.

Code R :

 
con<-url('https://www.sthda.com/upload/decathlon.rdata') # Create connexion
load(con) #Load the data
close(con) #close connexion
print(d) # Print the data

Download file from internet using R

To download a file from the Internet with R, we can use the function : download.file :

Code R :

 
download.file(url='https://www.sthda.com/upload/decathlon.rdata', 
                         destfile ="decathlon.rdata")

The file will be downloaded and saved in the current directory with the name decathlon.rdata

XLConnect : read, write and manipulate Microsoft Excel files from within R

Fri, 27 Jul 2012 19:00:00 +0200

XLConnect is a package that allows for reading, writing and manipulating Microsoft Excel files from within
R.

It does not require any installation of Microsoft Excel or any other special drivers to be able to read & write Excel files. The only requirement is a recent version of a Java Runtime Environment (JRE).

In order to get started have a look at the package vignette, the numerous demos available via demo(package = "XLConnect") or browse through the comprehensive reference manual.

Installation

Software Requirements

R, version 2.10.0 or higher
Java Runtime Environment (JRE), version 6.0 or higher

if you don't have JRE on your computer, you have to install it :
on linux /ubuntu use this command : apt-get install openjdk-6-jdk

Package Installation

XLConnect can be easily installed by using the install.packages() command in your R session:

Code R :

install.packages("XLConnect")

Writing Excel files

Basic functions

Code R :

 
#loading the package
require(XLConnect)
 
#creating an Excel workbook. Both .xls and .xlsx file formats can be used.
wb <- loadWorkbook("XLConnectExample1.xlsx", create = TRUE)
 
#creating sheets within an Excel workbook
createSheet(wb, name = "chickSheet")
 
#writing into sheets within an Excel workbook : 
#writing ChickWeight data frame into chickSheet
writeWorksheet(wb, ChickWeight, sheet = "chickSheet", startRow = 3, startCol = 4)
 
#saving a workbook to an Excel file :
#saves a workbook to the corresponding Excel file and writes the file to disk.
saveWorkbook(wb)

Writing sheet with one call

The four lines of code presented in the previous example can be replaced with a single call of the
writeWorksheetToFile() function:

Code R :

 
require(XLConnect)
writeWorksheetToFile("XLConnectExample2.xlsx", data = ChickWeight, 
                                 sheet = "chickSheet", startRow = 3, startCol = 4)

writeWorksheetToFile() loads the workbook, creates the sheet and finally saves the workbook. When you only need to write one sheet into an Excel file, this is probably the better choice. If you need to write more sheets, however, using the functions presented in the previous example will be more efficient. This is because calling writeWorksheetToFile() multiple times will open, write and close the Excel file with each call. Using the functions in the first example will, in contrast, allow you to open the workbook, do multiple operations on it and only then close it.

Reading from an Excel sheet

For this purpose, we will use the file created in the above example. We set the endRow argument to 10, to limit the result. We set the rest of arguments specifying boundaries as 0, so that they are automatically determined.
Please note, that alternatively to setting the sheet argument to the name of the sheet we want to read from, "chickSheet", we could also specify it with the sheet index, as sheet = 1.

Basic functions

Code R :

 
#loading the package
require(XLConnect)
 
#Loading an Excel workbook. Both .xls and .xlsx file formats can be used.
wb = loadWorkbook("XLConnectExample1.xlsx", create = TRUE)
 
#reading worksheets of an Excel workbook
data = readWorksheet(wb, sheet = "chickSheet", startRow = 0, endRow = 10,
startCol = 0, endCol = 0)
 
#print data
data

  weight Time Chick Diet
1     42    0     1    1
2     51    2     1    1
3     59    4     1    1
4     64    6     1    1
5     76    8     1    1
6     93   10     1    1
7    106   12     1    1

Reading from an Excel sheet with one call

Code R :

 
require(XLConnect)
data = readWorksheetFromFile("XLConnectExample1.xlsx", sheet = "chickSheet", 
startRow = 0, endRow = 10, startCol = 0, endCol = 0)

Adds an image to a worksheet using a named region

Code R :

 
# Load workbook (create if not existing)
wb = loadWorkbook("add_image_to_excel.xls", create=TRUE)
 
# Create a sheet named 'boxplot'
createSheet(wb, name = "boxplot")
 
# Create a named region called 'boxplot' referring to the sheet
# called 'boxplot' 
createName(wb, name = "boxplot", formula = "boxplot!$B$2")
 
# Create R plot to a png device
png(filename = "boxplot.png", width = 800, height = 600)
boxplot(count ~ spray, data = InsectSprays, col = "lightgray")
dev.off()
 
# Write image to the named region created above
addImage(wb, filename = "boxplot.png", name="boxplot", originalSize = TRUE)
 
# Save workbook (this actually writes the file to disk)
saveWorkbook(wb)

As a result, we obtain the following graph, written into Excel file

fgui: Generating automatically a GUI (graphical user interface) with R software

Wed, 25 Jul 2012 21:36:01 +0200

fgui is an R package to automatically generate a graphical interface for function arguments.
You just have to create your function and pass it to fgui. The interface will be automatically created by fgui library!

install fgui package

Code R :

 
install.packages('fgui')

xamples of using fgui

Quick example: create a GUI for a function that adds or multiplies two numbers x and y

Code R :

 
#1-Loading the package
require(fgui)
 
#2- add or multiplie (if multiplie =TRUE) two numbers and return the value
add <- function(x,  y, multiply) {
 if(multiply) return(x*y)  else return(x + y)
}
 
# Executing the function with a GUI
y <- gui(add,argOption=list(multiply=c("TRUE","FALSE")))

The generated image is as follows:

The codes in this tutorial have been tested and validated on MAC OSX /R.2.13 and R.2.15.1

Source :
http://www.r-bloggers.com/fgui-automatically-creating-widgets-for-arguments-of-a-function-%E2%80%93-a-quick-example/

Install samr package

Wed, 25 Jul 2012 12:15:01 +0200

SAM (Significance Analysis of Microarrays) is a statistical method to identify differentially expressed genes using microarray experiment.

To see the official website click here

To use SAM in R, install the package samr :

Code R :

 
install.packages('samr')

samr package depends on the 'inpute' package which can not be installed directly from R terminal (R 2.15.1 version).

inpute package is available from Bioconductor web site

To install the package inpute, use the following code in R :

Code R :

 
source("http://bioconductor.org/biocLite.R")
biocLite("impute")

Last articles - STHDA : R

R2DOCX : Create a word document with R

Pandoc : Convert Markdown documents to other formats

Create a Word document with R2DOCX

Installation

The available functions

Your first document

Create a Word document from template

Main title

Table of contents

Add texts (Normal et list)

Conditionnal formating of the text

Add a table

Add a plot

Text replacement

Heading styles available in your document

A full word document

Create an animated .gif image with R and ImageMagick

Example 1: Create a countdown

R code

Result

Example 2: Creating a 3D animated graphic

R code

Result

Loading data in R from internet

Importing a *. txt file from the Internet

Load .rdata file from internet

Download file from internet using R

XLConnect : read, write and manipulate Microsoft Excel files from within R

Installation

Software Requirements

Package Installation

Writing Excel files

Basic functions

Writing sheet with one call

Reading from an Excel sheet

Basic functions

Reading from an Excel sheet with one call

Adds an image to a worksheet using a named region

fgui: Generating automatically a GUI (graphical user interface) with R software

install fgui package

xamples of using fgui

Quick example: create a GUI for a function that adds or multiplies two numbers x and y

Install samr package