RISmed软件包的使用(pubmed文章批量查询与获取)

特别好用的工具RISmed包:可批量查询、获取、分析pubmed的文章,它很好的对接pubmed功能,可根据MESH、title、abstract、author等进行查询。

使用这个RISmed包需要先安装ggplot2,RColorBrewer,ggsci,因为在可视化的过程中需要用到。

1.R4.3.3(Linux)目前不兼容,报错如下



Ref:https://stackoverflow.com/questions/77608151/error-with-eutilssummary-in-rismed-package-length-4-coercion-issue

2.成功运行的代码记录如下:

R version 3.6.3 (2020-02-29),Windows system

#install.packages("RISmed")
#install.packages("RColorBrewer")
library(RISmed)
library(XML)
library(methods)
library(RColorBrewer)
##限定下检索主题
search_topic <- c('intracranial aneurysm' )
# search_topic <- "Valproic+acid|Valproate[Title/Abstract]+ALDH5A1[Title/Abstract]" #可根据title/ab等信息
# https://stackoverflow.com/questions/32994991/r-package-rismed-different-results-using-the-eutilsget-or-summary-function
search_query <- EUtilsSummary(search_topic,db="pubmed", retmax=100,datetype='pdat', mindate=2019, maxdate=2020)
##查查看下检索内容
summary(search_query)
##看下这些文献的Id
QueryId(search_query)
##获取检索结果
records <- EUtilsGet(search_query)
class(records)
str(records)
##提取检索结果
pubmed_data <- data.frame('Title'=ArticleTitle(records),
'Year'=YearAccepted(records),
'journal'=ISOAbbreviation(records))
head(pubmed_data,1)
pubmed_data[1:3,1]
write.csv(pubmed_data,file='DNA_methylation_in_plant.csv')
##分析文章情况
y <- YearPubmed(EUtilsGet(search_query))
##可视化一下
library(ggplot2)
date()
count <- table(y)
count <- as.data.frame(count)
names(count)<-c("Year", "Counts")
library(ggsci)
ggplot(data=count, aes(x=Year, y=Counts,fill=Year)) +
geom_bar(stat="identity", width=0.5)+
labs(y = "Number of articles",title="PubMed articles containing intracranial aneurysm"
) + theme_bw() + scale_fill_manual(values = **colorRampPalette(brewer.pal(19, "Accent"))(19)**) + ##color设置
theme(legend.position="bottom")

3.对颜色(color)设置的笔记

library(RColorBrewer)
cols <- brewer.pal(8,"Set2") #"Set1","Set3","Set4" #不同颜色设置
cols <-colorRampPalette(brewer.pal(9,”Blues”))(100) #一个颜色的渐变色设置
#一些配色方案:
cols <- colorRampPalette(brewer.pal(10, "Accent"))(10))
cols <- colorRampPalette(brewer.pal(19, "Accent"))(19)**)
# 根据Rstudio的提示稍微更改一下参数,得到的图片就会相应的改变
ggplot(data=count, aes(x=Year, y=Counts,fill=Year)) +
geom_bar(stat="identity", width=0.5)+
labs(y = "Number of articles",title="PubMed articles containing intracranial aneurysm"
) + theme_bw() + scale_fill_manual(values = **cols**) +
theme(legend.position="bottom")

参考:https://www.r-bloggers.com/2010/12/r-using-rcolorbrewer-to-colour-your-figures-in-r/

转自:https://www.jingege.wang/2020/06/03/pubmed数据挖掘:rismed包/

posted @   corrschi  阅读(237)  评论(0编辑  收藏  举报
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