From bc9e21739d7d25e834885d3d6066292dc883e75c Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Tue, 10 Jul 2018 16:52:01 +0200
Subject: [PATCH] title
---
server.R | 80 ++++++++++++++++++++++++++++++++++++++++----------------
1 file changed, 57 insertions(+), 23 deletions(-)
diff --git a/server.R b/server.R
index e9ea894..501af28 100644
--- a/server.R
+++ b/server.R
@@ -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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