get() calls on input$z column throwing error

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英文:

get() calls on input$z column throwing error

问题

我正试图复制来自此评论中的解决方案,使用Shiny应用程序中的响应式输入值,但似乎无法使dr4pl识别输入值作为数据列。我尝试将输入分配为变量,使用data[[]]对其进行子集化等。

我创建了一个包含链接中示例数据的CSV文件。

!曲线
C1
C1
C1
C1
C1
C1
C1
C1
C1
C2
C2
C2
C2
C2
C2
C2
C2
C2
C3
C3
C3
C3
C3
C3
C3
C3
C3

!POC
1.07129314
0.9112628
0.97914297
0.95904437
0.8850967
0.84338263
0.75843762
0.61319681
0.52635571
0.84563087
1.24435113
1.11757648
0.82383523
0.82763447
0.72585483
0.31953609
0.15056989
0.10057988
0.57384256
0.65984339
0.81439758
0.84572057
0.62797088
0.30800934
0.08957274
0.06360764
0.04451161

!剂量
0.078125
0.15625
0.3125
0.625
1.25
2.5
5
10
20
0.078125
0.15625
0.3125
0.625
1.25
2.5
5
10
20
0.078125
0.15625
0.3125
0.625
1.25
2.5
5
10
20

编辑:之前的错误是因为我忘记了使用get(),导致被调用的值为空。

当前错误

    Error in ==: comparison (==) is possible only for atomic and list types

ColID似乎失去了input$z的完整上下文?ColID的类别与示例相同,所以不确定我漏掉了什么。

library(shiny)
library(tidyverse)
library(plotly)
library(dr4pl)
library(data.table)

ui <- fluidPage(# 应用程序标题
  sidebarLayout(
    sidebarPanel(
      fileInput('file', "选择CSV文件"),
      uiOutput('X_dropdown'),
      uiOutput('Y_dropdown'),
      uiOutput('Z_dropdown'),
      uiOutput('IC50_Checkbox'),
    ),
    
    mainPanel(plotlyOutput("Plot"),
              plotlyOutput("P_IC50_table"))
  ))

# 定义绘制图形所需的服务器逻辑
server <- function(input, output, session) {
  # 将上传的文件保存为响应式输出,文件可以更改
  dta <- reactive({
    req(input$file)
    read.csv(input$file$datapath, header = T)
  })
  
  output$X_dropdown <- renderUI({
    req(dta())
    selectInput('x', "X", names(dta()), selected = "dose")
  })
  output$Y_dropdown <- renderUI({
    req(dta())
    selectInput('y', "Y", names(dta()), selected = "POC")
  })
  output$Z_dropdown <- renderUI({
    req(dta())
    selectInput('z', "颜色", names(dta()), selected = "curve")
  })
  output$IC50_Checkbox <- renderUI({
    req(dta())
    checkboxInput("ic50", "计算ICXX?", value = F)
  })
  
  output$Plot <- renderPlotly({
    req(dta())
    req(input$x)
    
    if (input$ic50 == T) {
      # 分配函数给变量
      
      multiIC <- function(data, 
                          colDose, colResp, colID, 
                          inhib.percent, 
                          ...) 
      {
        # 获取曲线ID
        
        locID <- unique(data[[colID]])
        
        # 准备一个向量来存储IC50
        locIC <- rep(NA, length(locID))
        
        # 为每个曲线单独计算IC50
        for (ii in seq_along(locID)) {
          # 子集一个剂量响应
          locSub <- data[get(colID) == locID[[ii]], ]
          
          # 计算IC50
          locIC[[ii]] <- dr4pl::IC(
            dr4pl::dr4pl(dose = locSub[[colDose]], 
                         response = locSub[[colResp]],
                         ...), 
            inhib.percent)
        }
        
        return(data.frame(id = locID,
                          x = locIC))
      }
      # 更改数据
      dfIC50 <- multiIC(data = dta(),
                        colDose = input$x,
                        colResp = input$y,
                        colID = input$z,
                        inhib.percent = 50              
      )
      #browser()
      IC50_table <- data.frame(id = locID, x = locIC)
      
      ggplotly(
        width = 500,
        height = 500,
        ggplot(data = dta(),
               aes(
                 x = .data[[input$x]],
                 y = .data[[input$y]],
                 color = as.factor(.data[[input$z]])
               )) +
          labs(color = "") +
          geom_vline(data = IC50_table, aes(xintercept = x))
      )
      
      output$P_IC50_table <- renderTable({
        # 尝试添加IC50曲线
        IC50_table
      })
    } else{}
  })
}

# 运行应用程序
shinyApp(ui = ui, server = server)
英文:

I'm trying to replicate the solution from this comment
using reactive input values through the shiny app, but I can't seem to get dr4pl to recognize the input values as a column of data. I've tried assigning input as a variable, subsetting it with data[[]], etc.

I've created a CSV that contains the example data in the link.

>! curve
C1
C1
C1
C1
C1
C1
C1
C1
C1
C2
C2
C2
C2
C2
C2
C2
C2
C2
C3
C3
C3
C3
C3
C3
C3
C3
C3

>! POC
1.07129314
0.9112628
0.97914297
0.95904437
0.8850967
0.84338263
0.75843762
0.61319681
0.52635571
0.84563087
1.24435113
1.11757648
0.82383523
0.82763447
0.72585483
0.31953609
0.15056989
0.10057988
0.57384256
0.65984339
0.81439758
0.84572057
0.62797088
0.30800934
0.08957274
0.06360764
0.04451161

>! dose
0.078125
0.15625
0.3125
0.625
1.25
2.5
5
10
20
0.078125
0.15625
0.3125
0.625
1.25
2.5
5
10
20
0.078125
0.15625
0.3125
0.625
1.25
2.5
5
10
20

Edit: The previous error was due to me forgetting the get(), leading to the values called being empty.

Current error

    Error in ==: comparison (==) is possible only for atomic and list types

ColID appears to lose the full context of input$z? The class of ColID is the same as the example, so not sure what I'm missing

library(shiny)
library(tidyverse)
library(plotly)
library(dr4pl)
library(data.table)
ui &lt;- fluidPage(# Application title
sidebarLayout(
sidebarPanel(
fileInput(&#39;file&#39;, &quot;Choose CSV File&quot;),
uiOutput(&#39;X_dropdown&#39;),
uiOutput(&#39;Y_dropdown&#39;),
uiOutput(&#39;Z_dropdown&#39;),
uiOutput(&#39;IC50_Checkbox&#39;),
),
mainPanel(plotlyOutput(&quot;Plot&quot;),
plotlyOutput(&quot;P_IC50_table&quot;))
))
# Define server logic required to draw graph
server &lt;- function(input, output, session) {
#saves uploaded file as a reactive output, file can be changed
dta &lt;- reactive({
req(input$file)
read.csv(input$file$datapath, header = T)
})
output$X_dropdown &lt;- renderUI({
req(dta())
selectInput(&#39;x&#39;, &quot;X&quot;, names(dta()), selected = &quot;dose&quot;)
})
output$Y_dropdown &lt;- renderUI({
req(dta())
selectInput(&#39;y&#39;, &quot;Y&quot;, names(dta()), selected = &quot;POC&quot;)
})
output$Z_dropdown &lt;- renderUI({
req(dta())
selectInput(&#39;z&#39;, &quot;Color&quot;, names(dta()), selected = &quot;curve&quot;)
})
output$IC50_Checkbox &lt;- renderUI({
req(dta())
checkboxInput(&quot;ic50&quot;, &quot;Calculate ICXX?&quot;, value = F)
})
output$Plot &lt;- renderPlotly({
req(dta())
req(input$x)
if (input$ic50 == T) {
#Assign functions to variables
multiIC &lt;- function(data, 
colDose, colResp, colID, 
inhib.percent, 
...) 
{
# Get curve IDs
locID &lt;- unique(data[[colID]])
# Prepare a vector to store IC50s
locIC &lt;- rep(NA, length(locID))
# Calculate IC50 separately for every curve
#seq_along takes the length of the sequence
for (ii in seq_along(locID)) {
# Subset a single dose response
locSub &lt;- data[get(colID) == locID[[ii]], ]
# Calculate IC50
locIC[[ii]] &lt;- dr4pl::IC(
dr4pl::dr4pl(dose = locSub[[colDose]], 
response = locSub[[colResp]],
...), 
inhib.percent)
}
return(data.frame(id = locID,
x = locIC))
}
#changed data
dfIC50 &lt;- multiIC(data = dta(),
colDose = input$x,
colResp = input$y,
colID = input$z,
inhib.percent = 50              
)
#browser()
IC50_table &lt;- data.frame(id = locID, x = locIC)
ggplotly(
width = 500,
height = 500,
ggplot(data = dta(),
aes(
x = .data[[input$x]],
y = .data[[input$y]],
color = as.factor(.data[[input$z]])
)) +
labs(color = &quot;&quot;) +
geom_vline(data = IC50_table, aes(xintercept = x))
)
output$P_IC50_table &lt;- renderTable({
#Attempt to add in IC50 curve
IC50_table
})
} else{}
})
}
# Run the application
shinyApp(ui = ui, server = server)

答案1

得分: 1

你能在应用程序初始化时打印出dta()和input的值吗?我怀疑它们不太对。如果你手动运行multiIC函数并使用固定值,是否会得到预期的响应?

你的multiIC函数中也缺少locSub()中的get()和LocID()中的unique()。

英文:

Can you print the values dta() and input on app initialization. I suspect they are not quite right. if you manually run the multiIC function with fixed values does it give expected response?

Your multiIC is also missing get() in locSub() and unique() in LocID()

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  • 本文由 发表于 2023年6月15日 00:52:06
  • 转载请务必保留本文链接:https://go.coder-hub.com/76475891.html
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