EditR_wang/ui.R at main · since25/EditR_wang · GitHub

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ui <- fluidPage(
  tags$head(
    tags$style(HTML("
      .container-fluid {
        max-width: 1480px;
      }
      .table-wrap {
        display: block;
        overflow-x: scroll;
        overflow-y: hidden;
        width: 100%;
        margin-bottom: 12px;
        padding-bottom: 6px;
        border: 1px solid #e5e5e5;
        border-radius: 4px;
        background: #fff;
      }
      .table-wrap table {
        display: table;
        font-size: 12px;
        white-space: nowrap;
        width: max-content;
        min-width: 100%;
        margin-bottom: 0;
      }
      .table-wrap table th,
      .table-wrap table td,
      table.dataTable th,
      table.dataTable td {
        text-align: center !important;
        vertical-align: middle !important;
      }
      .shiny-plot-output {
        width: 100% !important;
      }
      .section-header {
        display: flex;
        align-items: center;
        justify-content: space-between;
        gap: 12px;
      }
      .section-header h4 {
        margin: 0;
      }
    "))
  ),
  titlePanel("AB1 文件分析工具"),

  sidebarLayout(
    sidebarPanel(
      width = 3,
      helpText("用于碱基编辑的 AB1 / Sanger 测序分析。程序会自动识别输入序列与测序结果的正反向关系；选择目标碱基和编辑后碱基后，可输出摘要、位点编辑率图和下载结果。分析结果与 ab1 测序质量相关，结果异常时建议导入 SnapGene 查看峰图。"),
      textInput("template_filter", "搜索模板标签", value = ""),
      selectInput("saved_sequence", "已保存序列模板", choices = c("请选择已保存序列模板" = "")),
      textInput("sequence", "输入序列", value = ""),  # 序列输入框
      textInput("template_name", "模板标签（例如 RD-201-DIS3）", value = ""),
      textInput("target_position", "重点目标位点（例如 8）", value = ""),
      actionButton("save_template", "保存当前序列模板"),
      actionButton("delete_template", "删除当前模板"),
      helpText("选择需要统计的参考碱基位点。程序会在输入序列中找出所有该碱基位置，并提取这些位点的峰比例。"),
      selectInput("target_base", "目标碱基", choices = c("A", "C", "G", "T"), selected = "C"),
      helpText("选择期望的编辑后碱基。程序会输出每个位点的目标碱基比例、编辑后碱基比例、编辑率和 non-target edit rate。"),
      selectInput("edited_base", "编辑后碱基", choices = c("A", "C", "G", "T"), selected = "T"),
      helpText("处理前可先用正则规则规范样本名称，便于结果表和下载文件阅读。该操作只影响应用中的显示名称，不改动原始 ab1 文件。"),
      selectInput(
        "rename_preset",
        "文件名规则",
        choices = c(
          "仅去掉 .ab1 后缀" = "strip_extension",
          "去掉开头序号" = "strip_leading_index",
          "去掉测序公司 TSS 后缀" = "strip_tss_suffix",
          "保留 编号_引物名" = "keep_index_and_primer",
          "组合规则（保留编号_引物名）" = "combined_default",
          "自定义正则" = "custom"
        ),
        selected = "combined_default"
      ),
      textInput("rename_pattern", "正则表达式", value = ""),
      textInput("rename_replacement", "替换为", value = ""),
      selectInput("saved_regex", "已保存正则规则", choices = c("请选择已保存正则规则" = "")),
      textInput("regex_preset_name", "规则名称", value = ""),
      actionButton("save_regex", "保存正则规则"),
      actionButton("delete_regex", "删除选中规则"),
      textInput("download_tag", "Tag名称", value = ""),
      actionButton("preview_rename", "预览改名结果"),
      helpText("8个文件处理时间为90秒，文件越多时间越久，耐心等待"),
      fileInput("ab1_files", "上传 AB1 文件", multiple = TRUE, accept = ".ab1"),  # 文件上传按钮
      actionButton("process", "处理数据")  # 处理数据按钮
    ),

    mainPanel(
      width = 9,
      textOutput("status"),  # 状态信息
      verbatimTextOutput("task_progress"),  # 当前任务进度
      tabsetPanel(
        tabPanel(
          "分析概览",
          div(
            class = "section-header",
            h4("摘要"),
            downloadButton("download", "下载结果包（Excel + 图表）")
          ),
          helpText("Target_Position_Edit_Rate: 手动指定重点位点的预期编辑率。Top_Position_Edit_Rate: 最高编辑位点的预期编辑率。Non_Target_Edit_Rate_at_Top_Position: 历史字段，表示最高位点总非参考碱基比例（包含预期编辑）；非预期替换率与编辑产物纯度见对应新字段。"),
          div(class = "table-wrap", tableOutput("summary")),
          h4("图表"),
          uiOutput("summary_plot_ui"),
          selectInput("sample_plot_name", "单样本图选择", choices = c("请选择样本" = "")),
          plotOutput("sample_position_plot", height = "340px"),
          plotOutput("heatmap_plot", height = "460px")
        ),
        tabPanel(
          "文件名预览",
          div(class = "table-wrap", tableOutput("rename_preview")),
          downloadButton("download_renamed_ab1", "下载重命名AB1")
        )
      )
    )
  )
)