diff --git a/server.R b/server.R index 21f8e844d502fe7a331bdc9bbb9acd1226d02f29..7aa95a29831405abf33decccda763e4b548ebf2b 100644 --- a/server.R +++ b/server.R @@ -258,12 +258,13 @@ shinyServer is.null(checkNull(input$barGrid)), "", glue( - "p <- p + facet_grid(\". ~ {input$barGrid}\", scales = \"free_x\")" + "p <- p + facet_grid(\". ~ {input$barGrid}\", scales = \"free_x\") + " ) - ), + ), "\n", "plot(p)" - ) + ) }) output$histo <- renderPlot({ @@ -530,7 +531,65 @@ shinyServer "richnessShape", label = "Shape : ", choices = c("..." = 0, sample_variables(data16S())) - ) + ), + collapsedBox(verbatimTextOutput("richnessAScript"), title = "RCode") + ) + }) + + output$richnessAScript <- renderText({ + paste0( + scriptHead, + "# Plot boxplot of alpha diversity\n", + "p <- plot_richness(physeq = data", + ifelse( + is.null(checkNull(input$richnessX)), + "", + glue(", x = \"{input$richnessX}\"") + ), + ifelse( + is.null(checkNull(input$richnessColor)), + "", + glue(", color = \"{input$richnessColor}\"") + ), + ifelse( + is.null(checkNull(input$richnessShape)), + "", + glue(", shape = \"{input$richnessShape}\"") + ), + ifelse( + is.null(checkNull(input$richnessTitle)), + "", + glue(", title = \"{input$richnessTitle}\"") + ), + ifelse( + is.null(checkNull(input$richnessMeasures)), + "", + glue( + ", measures = c(\"{glue_collapse(input$richnessMeasures, sep='\", \"')}\")" + ) + ), + ")\n", + ifelse((input$richnessBoxplot >= 2), + "p <- p + geom_boxplot()\n", + ""), + ifelse((input$richnessBoxplot <= 2), + "p <- p + geom_point()\n", + ""), + "\n", + "plot(p)", + "\n", + "\n", + "# Tables\n", + glue("t <- estimate_richness(data"), + ifelse( + is.null(checkNull(input$richnessMeasures)), + "", + glue( + ", measures = c(\"{glue_collapse(input$richnessMeasures, sep='\", \"')}\")" + ) + ), + ")\n", + "write.table(t, file = \"richness.tsv\", sep = \"\\t\", col.names = NA)" ) }) @@ -565,6 +624,7 @@ shinyServer }) output$richnessBUI <- renderUI({ + validate(need(data16S(), "")) box( title = "Setting : " , width = NULL,