初学shiny，实现一个简单的功能：上传VCF文件，输出不同SNP数量图
shiny代码：
library(shiny)
library(vcfR)
library(tidyr)
library(ggplot2)
source("VCF.R")
# Define UI ----
ui <- fluidPage(
#titlePanel("title panel"),
fluidRow(
column(4,fileInput("counts", multiple = FALSE, accept = c(".vcf",".gz"), h3("Input your vcf file.")))
),
fixedRow(
column(4,actionButton("run", label = "Plot", icon = icon("paper-plane")))
),
hr(),
fixedRow(
column(1,downloadButton("downloadData", "Save PDF")),
column(1,downloadButton("downloadData1", "Save PNG")),
),
fixedRow(
mainPanel(plotOutput("map"))
)
)
# Define server logic ----
server <- function(input, output) {
td <- getwd()
options(shiny.maxRequestSize=100*1024^2)
data <- reactive({
## datapath is a must
req(input$counts$datapath)
})
observeEvent(input$run,{
output$map <- renderPlot({
#histogram('../mytest.vcf')
histogram(data())
})
})
output$downloadData <- downloadHandler(
filename = function() {
paste("p1", "pdf", sep = ".")
},
content = function(file) {
file.copy(paste0(td,"/p1.pdf"), file)
}
)
output$downloadData1 <- downloadHandler(
filename = function() {
paste("p1", "png", sep = ".")
},
content = function(file) {
file.copy(paste0(td,"/p1.png"), file)
}
)
}
# Run the app ----
shinyApp(ui = ui, server = server)
处理VCF文件脚本：
histogram <- function(var){
td <- getwd()
con <- file(var, "r")
line=readLines(con,n=1)
table = data.frame(
REF_ALT = c('AT','AG','AC','TG','TC','TA','GA','GT','GC','CA','CG','CT'),
NUM = 0
)
while( length(line) != 0 ) {
sta = startsWith(line, '#')
if(sta == TRUE){
}
else{
REF = c(strsplit(line, "t")[[1]][4])
ALT = c(strsplit(line, "t")[[1]][5])
table[which(table[,1]==paste0(REF,ALT)),2] <- table[which(table[,1]==paste0(REF,ALT)),2] + 1
}
line=readLines(con,n=1)
}
p <- ggplot(table,aes(REF_ALT,NUM))
k <- p+geom_bar(stat = 'identity',aes(fill=NUM))
ggsave(paste0(td,"/p1.pdf"),plot = k,dpi=300)
ggsave(paste0(td,"/p1.png"),plot = k,dpi=300)
close(con)
return(k)
}
效果：
