问题描述
我有这个数据框：
> df
genes enst x y
1 Gene1 ENST1 25 14
2 Gene1 ENST2 60 25
3 Gene1 ENST3 12 5
4 Gene2 ENST1 9 34
5 Gene2 ENST2 14 12
6 Gene3 ENST1 10 1
我正在尝试创建一个 Shiny 应用程序，它允许我选择基因和转录本。如果您选择一个基因（例如，Gene1），您将有一个选项来选择您想要的转录本（在这种情况下，ENST1、ENST2、ENST3）。
问题是我想绘制 2 个图。如果您单击“基因”（级别：基因），它将对来自该基因的所有值求和。 例如，对于具有 3 个转录本的第一个基因，x 的总值将为 20+60+12=92，y 的总值将为 14+25+5=44）。因此绘制基因 1 的值将是：x=92 和 y=44。
此外，我想绘制每个成绩单。例如，如果您选择“Gene1”和“Transcript 1”，绘图将使用 x=25 和 y=14。但是，如果用户决定选择两个成绩单，用户将看到 2 个图。或者如果用户选择 3 个成绩单，用户将看到 3 个不同的情节。
现在，用我的代码：
如果您选择基因，您将获得该基因的图。
但是，它会在同一情节中显示所有成绩单。我只想显示一份成绩单（或更多，如果用户需要）
我不知道如何继续。
另一方面，有两件事我不知道如何实现。
有人可以帮我吗？提前致谢
我的代码：
library(shiny)
################ DATA #############################
genes<- c("Gene1","Gene1","Gene2","Gene3")
enst <- c("ENST1","ENST2","ENST3","ENST1","ENST1")
x <- c(25,60,12,9,14,10)
y <- c(14,25,5,34,1)
df<- data.frame(genes,enst,x,y)
###################################################
ui <- fluidPage(
# Application title
titlePanel("Barplot"),sidebarLayout(
sidebarPanel(
uIoUtput("selected_gene"),uIoUtput("selected_transcript"),radioButtons("level","Level:",c("Gene" = "Gene","Transcript" = "Transcript")),h5(strong("If you want to see the plot,you have to click the button")),actionButton("add_plot","See the plot"),),mainPanel(
plotOutput("plot"),plotOutput("plot2"),tableOutput("table1"),tableOutput("table2")
)
)
)
server <- function(session,input,output) {
# This function gives us the list of genes.
genes_list <- reactive({
df$genes
})
transcripts_list <- reactive({
transcripts <- subset(df,df$genes==input$gene)
transcripts <- transcripts[,2]
return(transcripts)
})
# This function give us a select list input,in order to be able to select the gene that we want to see
output$selected_gene <- renderUI({
selectizeInput(inputId = "gene","Select one gene",choices=genes_list(),options=list(maxOptions = length(genes_list())))
})
output$selected_transcript <- renderUI({
selectizeInput(inputId = "transcript","Select one transcript",choices=transcripts_list(),options=list(maxOptions = length(transcripts_list())),multiple=T)
})
gene_values <- reactive({
values <- subset(df,df[1]==input$gene)
values$enst <- NULL
if(nrow(values)>1){ #for those genes who have more than 1 transcript
values_new <- values[2:length(values)]
values_new <- as.data.frame(t(colSums(values_new))) # sum the columns,transpose and transform into a dataframe
gene <- values[1,] #we take the first row,only one gene but all the info.
values <- cbind(values_new,gene[1]) # we bind both dataframes,however,we only want the gene name
values <- values[,c("genes",setdiff(names(values),"genes"))] # we move the last column at the beginning
}
return(values)
})
transc_values <- reactive({
values <- subset(df,df[1]==input$gene)
values$genes <- NULL
return(values)
})
plot_genes <- reactive({
gene_values <- gene_values()
barplot(c(gene_values$x,gene_values$y))
})
plot_transc <- reactive({
transc_values <- transc_values()
barplot(c(transc_values$x,transc_values$y))
})
v <- reactiveValues(plot = NULL)
observeEvent(input$add_plot,{
if(input$level == "Gene"){
v$plot <- plot_genes()
}
if(input$level == "Transcript"){
v$plot <- plot_transc()
}
})
# This function will draw the plot
# output$plot <- renderPlot({
# if (is.null(v$plot)){
# return()
# }
# v$plot
# })
output$table1 <- renderTable(gene_values())
output$table2 <- renderTable(transc_values())
output$plot <- renderPlot(plot_genes())
output$plot2 <- renderPlot(plot_transc())
}
shinyApp(ui,server)
解决方法
也许你可以从这个开始，根据你的需要进行修改。
library(shiny)
library(ggplot2)
library(DT)
################ DATA #############################
genes<- c("Gene1","Gene1","Gene2","Gene3")
enst <- c("ENST1","ENST2","ENST3","ENST1","ENST1")
x <- c(25,60,12,9,14,10)
y <- c(14,25,5,34,1)
df<- data.frame(genes,enst,x,y)
###################################################
ui <- fluidPage(
# Application title
titlePanel("Histogram"),sidebarLayout(
sidebarPanel(
uiOutput("selected_gene"),uiOutput("selected_transcript"),radioButtons("level","Level:",c("Gene" = "Gene","Transcript" = "Transcript")),h5(strong("If you want to see the plot,you have to click the button")),div(actionButton("add_plot","See the plot"),actionButton("table","See the table"),actionButton("clear","Clear All")
)
),mainPanel(
plotOutput("plot"),DTOutput("table")
)
)
)
server <- function(input,output,session) {
## This function gives us the list of genes.
genes_list <- reactive({
unique(df$genes)
})
transcripts_list <- reactive({
req(input$gene)
transcripts <- subset(df,df$genes==input$gene)
transcripts <- transcripts[,2]
return(unique(transcripts))
})
# This function give us a select list input,in order to be able to select the gene that we want to see
output$selected_gene <- renderUI({
selectizeInput(inputId = "gene","Select one gene",choices=genes_list(),options=list(maxOptions = length(genes_list())))
})
output$selected_transcript <- renderUI({
selectizeInput(inputId = "transcript","Select one transcript",choices=transcripts_list(),options=list(maxOptions = length(transcripts_list())),multiple=F)
})
gene_values <- reactive({
req(input$gene)
values <- subset(df,df[1]==input$gene)
values$enst <- NULL
if(nrow(values)>1){ #for those genes who have more than 1 transcript
values_new <- values[2:length(values)]
values_new <- as.data.frame(t(colSums(values_new))) # sum the columns,transpose and transform into a dataframe
gene <- values[1,] #we take the first row,only one gene but all the info.
values <- cbind(values_new,gene[1]) # we bind both dataframes,however,we only want the gene name
values <- values[,c("genes",setdiff(names(values),"genes"))] # we move the last column at the beginning
}
return(values)
})
transc_values <- reactive({
req(input$transcript)
values <- subset(df,df[2]==input$transcript)
values$genes <- NULL
return(values)
})
mydata <- reactive({
req(input$level)
if(input$level == "Gene"){
df <- req(gene_values())
}else if(input$level == "Transcript"){
df <- req(transc_values())
}else df <- NULL
df
})
# plot_genes <- reactive({
# gene_values <- req(gene_values())
# barplot(c(gene_values$x,gene_values$y))
#
# })
#
# plot_transc <- reactive({
# transc_values <- req(transc_values())
# barplot(c(transc_values$x,transc_values$y))
#
# })
v <- reactiveValues(plot = NULL,table=NULL)
observeEvent(input$add_plot,{
v$plot <- ggplot(mydata(),aes(x=x,y=y)) + geom_bar(stat = "identity")
v$table <- NULL ### display only plot
},ignoreInit = TRUE)
observeEvent(input$table,{
v$table <- req(mydata())
v$plot <- NULL ### display only table
},ignoreInit = TRUE)
observeEvent(input$clear,{
v$table <- NULL
v$plot <- NULL
},ignoreInit = TRUE)
## This function will draw the plot
output$plot <- renderPlot({ v$plot })
output$table <- renderDT({ v$table })
}
shinyApp(ui,server)