Commit 94ef920c authored by Midoux Cedric's avatar Midoux Cedric

networkBScript + heatmapScript

parent 71d1f93e
......@@ -578,8 +578,11 @@ shinyServer
script <- c(script, "", "# Tables")
script <- c(
script,
glue("t <- estimate_richness({glue_collapse(c(\"data\", measures), sep=', ')})"),
"write.table(t, file = \"richness.tsv\", sep = \"\\t\", col.names = NA)")
glue(
"t <- estimate_richness({glue_collapse(c(\"data\", measures), sep=', ')})"
),
"write.table(t, file = \"richness.tsv\", sep = \"\\t\", col.names = NA)"
)
return(glue_collapse(script, sep = "\n"))
})
......@@ -660,10 +663,12 @@ shinyServer
script <- c(script, "tipColor <- NULL")
}
script <-
c(script,
c(
script,
"",
"p1 <- ggplot(beta, aes(x = x, y = y, fill = distance))",
"p1 <- p1 + geom_tile()")
"p1 <- p1 + geom_tile()"
)
if (!is.null(checkNull(input$richnessBTitle))) {
script <- c(script,
glue("p1 <- p1 + ggtitle(\"{input$richnessBTitle}\")"))
......@@ -755,8 +760,38 @@ shinyServer
"Sample name" = "value",
sample_variables(data16S())
)
)
),
collapsedBox(verbatimTextOutput("networkBScript"), title = "RCode")
)
})
output$networkBScript <- renderText({
scriptArgs <- c("g",
"physeq = data",
"hjust = 2")
if (!is.null(checkNull(input$netwCol))) {
scriptArgs <- c(scriptArgs, glue("color = \"{input$netwCol}\""))
}
if (!is.null(checkNull(input$netwShape))) {
scriptArgs <- c(scriptArgs, glue("shape = \"{input$netwShape}\""))
}
if (!is.null(checkNull(input$netwLabel))) {
scriptArgs <- c(scriptArgs, glue("label = \"{input$netwLabel}\""))
}
if (!is.null(checkNull(input$netwTitle))) {
scriptArgs <- c(scriptArgs, glue("title = \"{input$netwTitle}\""))
}
script <- c(
scriptHead,
"# Plot samples network",
glue(
"g <- make_network(data, distance = \"{input$richnessBDist}\", max.dist = {input$netwMax}, keep.isolates = {input$netwOrphan})"
),
glue("p <- plot_network({glue_collapse(scriptArgs, sep=', ')})")
)
script <- c(script, "", "plot(p)")
return(glue_collapse(script, sep = "\n"))
})
output$networkB <- renderPlot({
......@@ -942,8 +977,48 @@ shinyServer
"median",
"centroid"
)
),
collapsedBox(verbatimTextOutput("heatmapScript"), title = "RCode")
)
})
output$heatmapScript <- renderText({
scriptArgs <-
c(
glue(
"prune_taxa(names(sort(taxa_sums(data), decreasing = TRUE)[1:{input$heatmapTopOtu}]), data)"
),
glue("distance = \"{input$heatmapDist}\""),
glue("method = \"{input$heatmapMethod}\""),
"low = \"yellow\"",
"high = \"red\"",
"na.value = \"white\""
)
if (!is.null(checkNull(input$heatmapX))) {
scriptArgs <-
c(scriptArgs, glue("sample.order = \"{input$heatmapX}\""))
}
if (!is.null(checkNull(input$heatmapTitle))) {
scriptArgs <-
c(scriptArgs, glue("title = \"{input$heatmapTitle}\""))
}
script <- c(
scriptHead,
"# Plot heatmap",
glue("p <- plot_heatmap({glue_collapse(scriptArgs, sep=', ')})")
)
if (!is.null(checkNull(input$heatmapGrid))) {
script <- c(
script,
glue(
"p <- p + facet_grid(\". ~ {input$heatmapGrid}\", scales = \"free_x\")"
)
)
}
script <- c(script, "", "plot(p)")
return(glue_collapse(script, sep = "\n"))
})
output$Heatmap <- renderPlot({
......
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