Commit c829848f authored by Midoux Cedric's avatar Midoux Cedric
Browse files

plot_tree

parent e23c17ac
......@@ -111,7 +111,6 @@ shinyServer
output$rarefactionMin <- renderText({
if (!is.null(input$fileBiom)) {
paste("(min sample =", format(min(sample_sums(data16S(
))), big.mark = " "), "reads)")
} else {
paste("(min sample =", 0, "reads)")
......@@ -729,16 +728,9 @@ shinyServer
radioButtons(
"treeRank",
label = "Niveau taxonomique légendé :",
choices = list(
choices = c(
aucun = "",
# rank_names(data16S()),
"Kingdom",
"Phylum",
"Class",
"Order",
"Family",
"Genus",
"Species",
rank_names(data16S()),
OTU = "taxa_names"
),
inline = TRUE
......@@ -751,6 +743,7 @@ shinyServer
value = 20
),
checkboxInput("treeRadial", label = "Arbre radial", value = FALSE),
checkboxInput("treeSample", label = "Show samples", value = TRUE),
if (!is.null(input$fileMeta)) {
selectInput(
"treeCol",
......@@ -779,11 +772,12 @@ shinyServer
physeq = prune_taxa(names(sort(
taxa_sums(data16S()), decreasing = TRUE
)[1:input$treeTopOtu]), data16S()),
method = ifelse(input$treeSample, "sampledodge", "treeonly"),
color = checkNull(input$treeCol),
shape = checkNull(input$treeShape),
size = "abundance",
label.tips = checkNull(input$treeRank),
sizebase = 2,
sizebase = 5,
ladderize = "left",
plot.margin = 0
)
......
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