将R Shining checkboxGroupInput与其他输入选项组合
我有这些将R Shining checkboxGroupInput与其他输入选项组合,r,checkbox,shiny,R,Checkbox,Shiny,我有这些数据我想使用R闪亮的服务器来散布绘图: library(dplyr) library(permute) set.seed(1) meta.df <- data.frame(gene_id=paste0("id",1:10),symbol=paste0("n",rep(permute::shuffle(5),2)),stringsAsFactors=F) clusters.df <- data.frame(cell=paste0("c",1:100),cluster=rep(
数据
我想使用R
闪亮的服务器来散布绘图
:
library(dplyr)
library(permute)
set.seed(1)
meta.df <- data.frame(gene_id=paste0("id",1:10),symbol=paste0("n",rep(permute::shuffle(5),2)),stringsAsFactors=F)
clusters.df <- data.frame(cell=paste0("c",1:100),cluster=rep(permute::shuffle(10),10),sample=paste0("s",rep(permute::shuffle(5),20)),stringsAsFactors=F)
mat <- matrix(rnorm(10*100),10,100,dimnames=list(meta.df$gene_id,clusters.df$cell))
tsne.obj <- Rtsne::Rtsne(t(mat))
tsne.df <- as.data.frame(tsne.obj$Y) %>% dplyr::rename(tSNE1=V1,tSNE2=V2) %>% cbind(clusters.df)
samples <- c("all",unique(clusters.df$sample))
samples.choices <- 1:length(samples)
names(samples.choices) <- samples
问题是它似乎没有实际选择样本
s,因此显示的绘图没有点
如果我简单地通过替换以下内容来消除sample
s选项code
,它会起作用:
col.idx <- which(colnames(mat) %in% dplyr::filter(clusters.df,sample %in% chosen.samples())$cell)
gene.df <- suppressWarnings(dplyr::left_join(tsne.df %>% dplyr::filter(sample %in% chosen.samples()),data.frame(cell=colnames(mat)[col.idx],value=mat[row.idx,col.idx],stringsAsFactors=F),by=c("cell"="cell")))
col.idx您的代码中有两个错误。第一个在checkboxGroupInput
而不是
checkboxGroupInput("samples.choice", "Samples",choices = samples.choices,selected=1)
应该是
checkboxGroupInput("samples.choice", "Samples",choices = names(samples.choices),selected="all")
第二个是scatter.plot()
是plotly对象
,因此您应该使用plotly::plotlyOutput(“嵌入”)
和output$Embedding,非常感谢@SBista。我还有几个问题你可能会碰巧帮我解决:1。如果我从终端窗口启动闪亮的应用程序,它将在浏览器中打开,绘图仅显示在页面的右上象限。有可能扩大吗?2.当我按下“保存”按钮时,生成的PDF包含两页,其中第二页为空白。有没有办法防止这种情况?“只保存一页的意思?”丹,你说的“扩展”是什么意思?它采用了可用的宽度。我指的是垂直空间
checkboxGroupInput("samples.choice", "Samples",choices = samples.choices,selected=1)
checkboxGroupInput("samples.choice", "Samples",choices = names(samples.choices),selected="all")
server <- function(input, output)
{
chosen.samples <- reactive({
validate(
need(input$samples.choice != "",'Please choose at least one of the sample checkboxes')
)
samples.choice <- input$samples.choice
if("all" %in% samples.choice) samples.choice <- samples[-which(samples == "all")]
samples.choice
})
output$gene_id <- renderUI({
selectInput("gene_id", "Gene ID", choices = unique(dplyr::filter(meta.df,symbol == input$symbol)$gene_id))
})
scatter.plot <- reactive({
if(!is.null(input$symbol) & !is.null(input$gene_id)){
# subset of data
gene.symbol <- input$symbol
gene.id <- input$gene_id
row.idx <- which(rownames(mat) == gene.id)
col.idx <- which(colnames(mat) %in% dplyr::filter(clusters.df,sample %in% chosen.samples())$cell)
gene.df <- suppressWarnings(dplyr::left_join(tsne.df %>% dplyr::filter(sample %in% chosen.samples()),data.frame(cell=colnames(mat)[col.idx],value=mat[row.idx,col.idx],stringsAsFactors=F),by=c("cell"="cell")))
scatter.plot <- plotly::plot_ly(marker=list(size=12),type='scatter',mode="markers",color=~gene.df$value,x=~gene.df$tSNE1,y=~gene.df$tSNE2,showlegend=F) %>%
plotly::layout(xaxis=list(title="tSNE1",zeroline=F,showticklabels=F),yaxis=list(title="tSNE2",zeroline=F,showticklabels=F))
scatter.plot
}
})
output$Embedding <- plotly::renderPlotly({
scatter.plot()
})
output$save <- downloadHandler(
filename = function() {
paste0(dplyr::filter(meta.df,symbol == input$symbol,gene_id == input$gene_id)$symbol,"_",dplyr::filter(meta.df,symbol == input$symbol,gene_id == input$gene_id)$gene_id,".pdf")
},
content = function(file) {
plotly::export(scatter.plot(),file=file)
}
)
}
ui <- fluidPage(
# App title ----
titlePanel("Results Explorer"),
# Sidebar layout with a input and output definitions ----
sidebarLayout(
# Sidebar panel for inputs ----
sidebarPanel(
# select samples
checkboxGroupInput("samples.choice", "Samples",choices = names(samples.choices),selected="all"),
# select gene symbol
selectInput("symbol", "Gene Symbol", choices = unique(meta.df$symbol)),
# select gene id
uiOutput("gene_id"),
# select plot type
selectInput("plot.type", "Plot Type", choices = c("tSNE","PCA")),
# save plot as html
downloadButton('save', 'Save as PDF')
),
# Main panel for displaying outputs ----
mainPanel(
# The plot is called Embedding and will be created in ShinyServer part
# plotOutput("Embedding")
plotly::plotlyOutput("Embedding")
)
)
)
shinyApp(ui = ui, server = server)