Commit bc9e2173 authored by Midoux Cedric's avatar Midoux Cedric

title

parent bf14e198
......@@ -27,7 +27,7 @@ shinyServer
options = list(
dom = "lBtip",
pageLength = 10,
lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
lengthMenu = list(c(10, 25, 50, 100, -1), list('10', '25', '50', '100', 'All')),
buttons = list(
'colvis',
list(
......@@ -172,6 +172,9 @@ shinyServer
choices = rank_names(data16S()),
inline = TRUE
),
textInput("barTitle",
label = "Title : ",
value = "OTU abundance barplot"),
selectInput(
"barGrid",
label = "Subplot : ",
......@@ -192,7 +195,8 @@ shinyServer
p <- plot_bar(
physeq = data16S(),
fill = input$barFill,
x = ifelse(is.null(checkNull(input$barX)), "Sample", input$barX)
x = ifelse(is.null(checkNull(input$barX)), "Sample", input$barX),
title = checkNull(input$barTitle)
)
if (!is.null(checkNull(input$barGrid))) {
p <-
......@@ -349,6 +353,20 @@ shinyServer
),
inline = TRUE
),
radioButtons(
"richnessBoxplot",
label = "Representation : ",
choices = list(
"Dots only" = 1,
"Dots and boxplot" = 2,
"Boxplot only" = 3
),
selected = 2,
inline = TRUE
),
textInput("richnessTitle",
label = "Title : ",
value = "Alpha diversity graphics"),
selectInput(
"richnessX",
label = "X : ",
......@@ -363,17 +381,6 @@ shinyServer
"richnessShape",
label = "Shape : ",
choices = c("..." = 0, sample_variables(data16S()))
),
radioButtons(
"richnessBoxplot",
label = "Representation : ",
choices = list(
"Dots only" = 1,
"Dots and boxplot" = 2,
"Boxplot only" = 3
),
selected = 2,
inline = TRUE
)
)
})
......@@ -388,6 +395,7 @@ shinyServer
)), "samples", input$richnessX),
color = checkNull(input$richnessColor),
shape = checkNull(input$richnessShape),
title = checkNull(input$richnessTitle),
measures = checkNull(input$richnessMeasures)
)
if (input$richnessBoxplot >= 2) {
......@@ -413,10 +421,13 @@ shinyServer
width = NULL,
status = "primary",
selectInput(
"richnessOrder",
"richnessBOrder",
label = "Sorting sample : ",
choices = c("..." = 0, sample_variables(data16S()))
)
),
textInput("richnessBTitle",
label = "Title : ",
value = "Beta diversity heatmap")
)
})
......@@ -426,11 +437,11 @@ shinyServer
beta <-
melt(as(distance(data16S(), method = input$richnessBDist), "matrix"))
colnames(beta) <- c("x", "y", "distance")
if (!is.null(checkNull(input$richnessOrder)))
if (!is.null(checkNull(input$richnessBOrder)))
{
new_factor = as.factor(get_variable(data16S(), input$richnessOrder))
new_factor = as.factor(get_variable(data16S(), input$richnessBOrder))
variable_sort <-
as.factor(get_variable(data16S(), input$richnessOrder)[order(new_factor)])
as.factor(get_variable(data16S(), input$richnessBOrder)[order(new_factor)])
L = levels(reorder(sample_names(data16S()), as.numeric(new_factor)))
beta$x <- factor(beta$x, levels = L)
beta$y <- factor(beta$y, levels = L)
......@@ -440,7 +451,7 @@ shinyServer
}
p <-
ggplot(beta, aes(x = x, y = y, fill = distance)) + geom_tile()
p <- p + theme(
p <- p + ggtitle(input$richnessBTitle) + theme(
axis.text.x = element_text(
angle = 90,
hjust = 1,
......@@ -469,6 +480,9 @@ shinyServer
checkboxInput("netwOrphan",
label = "Keep orphans",
value = TRUE),
textInput("netwTitle",
label = "Title : ",
value = "Beta diversity network"),
selectInput(
"netwCol",
label = "Color : ",
......@@ -507,7 +521,7 @@ shinyServer
shape = checkNull(input$netwShape),
label = checkNull(input$netwLabel),
hjust = 2,
title = NULL
title = checkNull(input$netwTitle)
)
return(p)
})
......@@ -530,6 +544,7 @@ shinyServer
step = 100,
#step = input$rarefactionStep,
color = checkNull(input$rarefactionColor),
label = checkNull(input$rarefactionLabel),
se = FALSE
)
if (!is.null(checkNull(input$rarefactionGrid))) {
......@@ -541,7 +556,7 @@ shinyServer
p + geom_vline(xintercept = min(sample_sums(data16S())),
color = "gray60")
}
return(p)
return(p + ggtitle(input$rarefactionTitle))
})
......@@ -559,11 +574,19 @@ shinyServer
# value = 100
# ),
checkboxInput("rarefactionMin", label = "Show min sample threshold", value = FALSE),
textInput("rarefactionTitle",
label = "Title : ",
value = "Rarefaction curves"),
selectInput(
"rarefactionColor",
label = "Color : ",
choices = c("..." = 0, sample_variables(data16S()))
),
selectInput(
"rarefactionLabel",
label = "Label : ",
choices = c("..." = 0, sample_variables(data16S()))
),
selectInput(
"rarefactionGrid",
label = "Subplot : ",
......@@ -578,6 +601,9 @@ shinyServer
title = "Setting : " ,
width = NULL,
status = "primary",
textInput("heatmapTitle",
label = "Title : ",
value = "Taxa heatmap by samples"),
selectInput(
"heatmapGrid",
label = "Subplot : ",
......@@ -637,6 +663,7 @@ shinyServer
)[1:input$heatmapTopOtu]), data16S()),
distance = input$heatmapDist,
method = input$heatmapMethod,
title = checkNull(input$heatmapTitle),
sample.order = checkNull(input$heatmapX),
low = "yellow",
high = "red",
......@@ -672,6 +699,9 @@ shinyServer
),
checkboxInput("treeRadial", label = "Radial tree", value = FALSE),
checkboxInput("treeSample", label = "Show samples", value = TRUE),
textInput("treeTitle",
label = "Title : ",
value = "Phylogenetic tree"),
selectInput(
"treeCol",
label = "Color : ",
......@@ -704,7 +734,8 @@ shinyServer
label.tips = checkNull(input$treeRank),
sizebase = 5,
ladderize = "left",
plot.margin = 0
plot.margin = 0,
title = checkNull(input$treeTitle)
)
if (checkNull(input$treeRadial)) {
return(p + coord_polar(theta = "y"))
......@@ -746,6 +777,9 @@ shinyServer
selected = "MDS",
choices = list("DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA")
),
textInput("acpTitle",
label = "Title : ",
value = "Samples ordination graphic"),
selectInput(
"acpLabel",
label = "Label : ",
......@@ -787,7 +821,7 @@ shinyServer
distance = input$acpDist
),
axes = as.numeric(input$acpAxes),
#c(1, 2),
title = checkNull(input$acpTitle),
color = checkNull(input$acpCol),
replicate = checkNull(input$acpRep),
shape = checkNull(input$acpShape),
......
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