Commit e23c17ac authored by Midoux Cedric's avatar Midoux Cedric
Browse files

Strain for tax_rank

parent 4cc07004
......@@ -72,7 +72,8 @@ shinyServer
"Order",
"Family",
"Genus",
"Species")
"Species",
"Strain")[1:length(rank_names(d))]
tax_table(d)[grep("unknown ", tax_table(d))] <- NA
#tax_table(d)[grep("Unclassified", tax_table(d))] <- NA
if (!is.null(input$fileMeta)) {
......@@ -211,16 +212,8 @@ shinyServer
radioButtons(
"focusRank",
label = "Niveau taxo :",
choices = list(
"Kingdom" = 1,
"Phylum" = 2,
"Class" = 3,
"Order" = 4,
"Family" = 5,
"Genus" = 6
),
inline = TRUE,
selected = 1
choices = rank_names(data16S())[-length(rank_names(data16S()))],
inline = TRUE
)
})
......@@ -230,9 +223,7 @@ shinyServer
selectInput(
"focusTaxa",
label = "Taxa :",
choices = unique(as.matrix(as.data.frame(
tax_table(data16S())
)[, as.integer(input$focusRank)])),
choices = unique(as.vector(tax_table(data16S())[, input$focusRank])),
selected = TRUE
)
})
......@@ -276,18 +267,17 @@ shinyServer
))
p <- plot_composition(
physeq = data16S(),
taxaRank1 = rank_names(data16S())[as.integer(input$focusRank)],
taxaRank1 = input$focusRank,
taxaSet1 = input$focusTaxa,
taxaRank2 = rank_names(data16S())[as.integer(input$focusRank) + 1],
taxaRank2 = rank_names(data16S())[which(rank_names(data16S())==input$focusRank) + 1],
numberOfTaxa = input$focusNbTaxa,
fill = rank_names(data16S())[as.integer(input$focusRank) + 1],
fill = rank_names(data16S())[which(rank_names(data16S())==input$focusRank) + 1],
x = ifelse(is.null(checkNull(input$focusX)), "Sample", input$focusX)
)
if (!is.null(checkNull(input$focusGrid))) {
p <-
p + facet_grid(paste(".", "~", input$focusGrid), scales = "free_x")
}
return(p)
})
......@@ -741,6 +731,7 @@ shinyServer
label = "Niveau taxonomique légendé :",
choices = list(
aucun = "",
# rank_names(data16S()),
"Kingdom",
"Phylum",
"Class",
......
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