Commit 71d1f93e authored by Midoux Cedric's avatar Midoux Cedric

richnessBScript

parent 8f94943f
......@@ -578,13 +578,8 @@ shinyServer
script <- c(script, "", "# Tables")
script <- c(
script,
glue(
"t <- estimate_richness({glue_collapse(c(\"data\", measures), sep=', ')})"
)
)
script <-
c(script,
"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"))
})
......@@ -632,10 +627,64 @@ shinyServer
),
textInput("richnessBTitle",
label = "Title : ",
value = "Beta diversity heatmap")
value = "Beta diversity heatmap"),
collapsedBox(verbatimTextOutput("richnessBScript"), title = "RCode")
)
})
output$richnessBScript <- renderText({
script <- c(
scriptHead,
"# Plot heatmap of beta diversity",
glue(
"beta <- melt(as(distance(data, method = \"{input$richnessBDist}\"), \"matrix\"))"
),
"colnames(beta) <- c(\"x\", \"y\", \"distance\")"
)
if (!is.null(checkNull(input$richnessBOrder))) {
script <- c(
script,
glue(
"new_factor = as.factor(get_variable(data, \"{input$richnessBOrder}\"))"
),
glue(
"variable_sort <- as.factor(get_variable(data, \"{input$richnessBOrder}\")[order(new_factor)])"
),
"L = levels(reorder(sample_names(data), as.numeric(new_factor)))",
"beta$x <- factor(beta$x, levels = L)",
"beta$y <- factor(beta$y, levels = L)",
"palette <- hue_pal()(length(levels(new_factor)))",
"tipColor <- col_factor(palette, levels = levels(new_factor))(variable_sort)"
)
} else {
script <- c(script, "tipColor <- NULL")
}
script <-
c(script,
"",
"p1 <- ggplot(beta, aes(x = x, y = y, fill = distance))",
"p1 <- p1 + geom_tile()")
if (!is.null(checkNull(input$richnessBTitle))) {
script <- c(script,
glue("p1 <- p1 + ggtitle(\"{input$richnessBTitle}\")"))
}
script <- c(
script,
glue(
"p1 <- p1 + theme(axis.text.x = element_text(angle = 90, hjust = 1, color = tipColor), axis.text.y = element_text(color = tipColor), axis.title.x = element_blank(), axis.title.y = element_blank())"
)
)
script <- c(script, "", "plot(p1 + scale_fill_gradient2())")
script <- c(script, "", "# Tables")
script <- c(
script,
glue("t <- distance(data, method = \"{input$richnessBDist}\")"),
"write.table(t, file = \"distance.tsv\", sep = \"\\t\", col.names = NA)"
)
return(glue_collapse(script, sep = "\n"))
})
output$richnessB <- renderPlot({
validate(need(data16S(),
"Requires an abundance dataset"))
......@@ -816,7 +865,7 @@ shinyServer
}
script <- c(
scriptHead,
"# Plot filtered barplot",
"# Plot rarefaction curves",
glue("p <- ggrare({glue_collapse(scriptArgs, sep=', ')})")
)
if (!is.null(checkNull(input$rarefactionGrid))) {
......
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