From ece485dbb8752343ca48f6195034f1ba74e9d69b Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Tue, 11 Sep 2018 17:24:16 +0200
Subject: [PATCH] richnessAScript
---
server.R | 68 ++++++++++++++++++++++++++++++++++++++++++++++++++++----
1 file changed, 64 insertions(+), 4 deletions(-)
diff --git a/server.R b/server.R
index 21f8e84..7aa95a2 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,
--
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