This post, I wanted to create a word cloud (also called tag cloud) figure for Karen’s paper. I chose papers with Karen’s name since 2008, copied their title and abstract and saved in a plain text file called abstract_Karen2008.txt.
For the creation of figure, I used R and two packages tm (text mining) and wordcloud2. There is another package wordcloud, but it has been updated since 2013, so I did not use that one.
The basic idea is:
- read text.
- remove some unnecessary words and do some modifications.
- generate a dataframe with word and their frequency.
- draw word cloud figure.
First is to load packages and import text.
require(tm);require(wordcloud2)
# load text
text <- readLines("abstract_Karen2008.txt")
# Load the data as a corpus
docs <- Corpus(VectorSource(text))
# if need to see data, use inspect(docs)
# if need to manual change some words to space, use following function.
#toSpace <- content_transformer(function (x , pattern) gsub(pattern, " ", x))
#docs <- tm_map(docs, toSpace, ",")
#docs <- tm_map(docs, toSpace, "~")
#docs <- tm_map(docs, toSpace, "\\(")
#docs <- tm_map(docs, toSpace, "\\)")
#docs <- tm_map(docs, toSpace, "\\.")
Second, clean unnecessary words.
# Convert the text to lower case
docs <- tm_map(docs, content_transformer(tolower))
# Remove numbers
docs <- tm_map(docs, removeNumbers)
# Remove english common stopwords
docs <- tm_map(docs, removeWords, stopwords("english"))
# Remove your own stop word
# specify your stopwords as a character vector
rm_words <- c("bp","diatoms","also","via","many","near","genes",
"plants","can","results","using","hkme","within","likely",
"reveals","may")
docs <- tm_map(docs, removeWords, rm_words)
# Remove punctuations
docs <- tm_map(docs, removePunctuation)
# Eliminate extra white spaces
docs <- tm_map(docs, stripWhitespace)
Third, generate a word frequency dataframe.
# generate the word frequency dataframe
dtm <- TermDocumentMatrix(docs)
m <- as.matrix(dtm)
v <- sort(rowSums(m),decreasing=TRUE)
d <- data.frame(word = names(v),freq=v)
d$word <- as.character(d$word)
d["dna",][1] <- "DNA"
d["rna",][1] <- "RNA"
d["mop",][1] <- "MOP"
d$word <- as.factor(d$word)
head(d, 5)
Fourth, plotting.
# draw wordcloud with all names horizontal.
wordcloud2(data = d,size = 0.5,minRotation = 0, maxRotation = 0, minSize = 10,
rotateRatio = 1)
