词云Word Clouds的R实现

缘起：这是生信技能树公众号里Jimmy大神布置的一道作业：把tcga大计划的CNS级别文章标题画一个词云。我看着代码不难，感觉自己应该可以完成，就偷偷地尝试了起来。做完才发现，我的感觉是对的。

制作词云主要分为5个步骤：

• Step 1: Create a text file
• Step 2 : Install and load the required packages
• Step 3 : Text mining
• Step 4 : Build a term-document matrix
• Step 5 : Generate the Word cloud

具体步骤及代码：

Step 1: Create a text file

• Copy and paste the text in a plain text file (e.g : ml.txt)
• Save the file

本次作业所需的.txt文本来源于两个网页罗列的和TCGA相关的CNS文献标题，第一个在：2018的TCGA的泛癌项目论文全部是发表在Cell及其子刊上；第二个在：2020的Nature及其子刊的22篇全基因组的泛癌分析(Pan-Cancer Analysis of Whole Genomes)

Step 2 : Install and load the required packages

# Install
install.packages("tm")  # for text mining
install.packages("SnowballC") # for text stemming
install.packages("wordcloud") # word-cloud generator 
install.packages("RColorBrewer") # color palettes
# Load
library("tm")
library("SnowballC")
library("wordcloud")
library("RColorBrewer")

Step 3 : Text mining
3.1 Load the text

# import the text file created in Step 1
text <- readLines(file.choose())

# Load the data as a corpus
docs <- Corpus(VectorSource(text))

# Inspect the content of the document
inspect(docs)

3.2 Text transformation

toSpace <- content_transformer(function (x , pattern ) gsub(pattern, " ", x))
docs <- tm_map(docs, toSpace, "/")
docs <- tm_map(docs, toSpace, "@")
docs <- tm_map(docs, toSpace, "\\|")

3.3 Cleaning the text

# 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
docs <- tm_map(docs, removeWords, c("blabla1", "blabla2")) 
# Remove punctuations
docs <- tm_map(docs, removePunctuation)
# Eliminate extra white spaces
docs <- tm_map(docs, stripWhitespace)
# Text stemming
# docs <- tm_map(docs, stemDocument)

Step 4 : Build a term-document matrix

dtm <- TermDocumentMatrix(docs)
m <- as.matrix(dtm)
v <- sort(rowSums(m),decreasing=TRUE)
d <- data.frame(word = names(v),freq=v)
head(d, 10)

wordclouds1.jpg

Step 5 : Generate the Word cloud

set.seed(1234)
wordcloud(words = d$word, freq = d$freq, min.freq = 1,
          max.words=200, random.order=FALSE, rot.per=0.35, 
          colors=brewer.pal(8, "Dark2"))

效果图：

WordClouds.png

参考资料

文中参考代码链接在：Text mining and word cloud fundamentals in R : 5 simple steps you should know