我很难用rvest从COSMIC数据库中刮取MYC基因突变表。我只得到一个空清单。输出如下。我已经确认这些值在HTML文件中（即，不是JAVA，因为这些值在HTML文件本身中）。我还确认了我要抓取的元素是一张桌子。我尝试使用xpath和CSS。我还确认允许刮刮。请指教
R控制台输出
> library("rvest")
> library("dplyr")
> library("robotstxt")
> library("XML")
> library("RSelenium")
> library("splashr")
> library("reticulate")
> url = "https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=MYC#variants"
> paths_allowed(url)
cancer.sanger.ac.uk No encoding supplied: defaulting to UTF-8.
[1] TRUE
> Xpath = "//*[@id= 'DataTables_Table_0']"
> a = read_html(url) %>% html_nodes(xpath = Xpath) %>% html_table()
> a
list()
> Selector = "#DataTables_Table_0"
> a = read_html(url) %>% html_nodes(css = Selector) %>% html_table()
> a
list()
您可以执行网页请求以动态检索结果的相同请求（可在开发工具的网络选项卡中查看F12。）将DisplayLength参数更改为所有结果（1394）或将其设置为初始大数并检查返回值以捕获实际结果总结果计数并发出获取所有结果所需的任何其他请求。
虽然您可以执行简单的rvest请求
library(rvest)
url <- 'https://cancer.sanger.ac.uk/cosmic/gene/mutations?all_data=&coords=AA%3AAA&dr=&end=455&gd=&id=359910&ln=MYC&seqlen=455&src=gene&start=1&export=json&sEcho=2&iColumns=6&sColumns=&iDisplayStart=0&iDisplayLength=1394&mDataProp_0=0&sSearch_0=&bRegex_0=false&bSearchable_0=true&bSortable_0=true&mDataProp_1=1&sSearch_1=&bRegex_1=false&bSearchable_1=true&bSortable_1=true&mDataProp_2=2&sSearch_2=&bRegex_2=false&bSearchable_2=true&bSortable_2=true&mDataProp_3=3&sSearch_3=&bRegex_3=false&bSearchable_3=true&bSortable_3=true&mDataProp_4=4&sSearch_4=&bRegex_4=false&bSearchable_4=true&bSortable_4=true&mDataProp_5=5&sSearch_5=&bRegex_5=false&bSearchable_5=true&bSortable_5=true&sSearch=&bRegex=false&iSortCol_0=0&sSortDir_0=asc&iSortingCols=1'
r <- read_html(url) %>% html_node('p') %>% html_text()
write.table(r,file="data.txt", sep='\t', row.names = FALSE)
@Snehal Patel编辑到上面以获得所需的格式：
x = read.table("data.txt", sep = "\t", skip = 2, fill = TRUE)
colnames(x) = c("AA_Position", "CDS_Mutation", "AA_Mutation", "COSMIC_ID", "count", "Mutation_type")
使用httr，传递各种标头，并根据响应构造一个数据帧。
library(httr)
library(purrr)
library(rvest)
headers = c(
'X-Requested-With' = 'XMLHttpRequest',
'User-Agent' = 'Mozilla/5.0',
'Referer' = 'https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=MYC'
)
params = list(
'coords' = 'AA:AA',
'end' = '455',
'id' = '359910',
'ln' = 'MYC',
'seqlen' = '455',
'src' = 'gene',
'start' = '1',
'export' = 'json',
'sEcho' = '4',
'iColumns' = '6',
'iDisplayStart' = '0',
'iDisplayLength' = '1394', #for all results. You can set to number higher than you expect then check first result for actual
'mDataProp_0' = '0',
'bRegex_0' = 'false',
'bSearchable_0' = 'true',
'bSortable_0' = 'true',
'mDataProp_1' = '1',
'bRegex_1' = 'false',
'bSearchable_1' = 'true',
'bSortable_1' = 'true',
'mDataProp_2' = '2',
'bRegex_2' = 'false',
'bSearchable_2' = 'true',
'bSortable_2' = 'true',
'mDataProp_3' = '3',
'bRegex_3' = 'false',
'bSearchable_3' = 'true',
'bSortable_3' = 'true',
'mDataProp_4' = '4',
'bRegex_4' = 'false',
'bSearchable_4' = 'true',
'bSortable_4' = 'true',
'mDataProp_5' = '5',
'bRegex_5' = 'false',
'bSearchable_5' = 'true',
'bSortable_5' = 'true',
'bRegex' = 'false',
'iSortCol_0' = '0',
'sSortDir_0' = 'asc',
'iSortingCols' = '1'
)
r <- content(httr::GET(url = 'https://cancer.sanger.ac.uk/cosmic/gene/mutations', httr::add_headers(.headers=headers), query = params)) %>%
.$aaData
df <- map_df(r, function(i) {
data.frame(
`Position` = read_html(i[[1]]) %>% html_node('a') %>% html_text() %>% as.numeric() ,
`CDS Mutation` = read_html(i[[2]]) %>% html_node('a') %>% html_text(),
`AA Mutation` = read_html(i[[3]]) %>% html_node('a') %>% html_text(),
`Legacy Mutation ID` = i[[4]],
`Count` = i[[5]] ,
`Type` = i[[6]] ,
stringsAsFactors=FALSE)
})
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