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Cedric Midoux
Easy16S
Commits
58726f00
Commit
58726f00
authored
Dec 22, 2020
by
Cedric Midoux
Browse files
adonis
parent
894413b0
Changes
3
Hide whitespace changes
Inline
Side-by-side
panels/richnessB-server.R
View file @
58726f00
...
@@ -5,6 +5,7 @@ betaDist <- metaReactive2({
...
@@ -5,6 +5,7 @@ betaDist <- metaReactive2({
})
})
})
})
## MDS
output
$
betaMdsUI
<-
renderUI
({
output
$
betaMdsUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
validate
(
need
(
physeq
(),
""
))
box
(
box
(
...
@@ -100,6 +101,7 @@ observeEvent(input$betaMds_output_code,
...
@@ -100,6 +101,7 @@ observeEvent(input$betaMds_output_code,
}
}
)
)
## Cluster
output
$
betaClusterUI
<-
renderUI
({
output
$
betaClusterUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
validate
(
need
(
physeq
(),
""
))
box
(
box
(
...
@@ -142,6 +144,34 @@ observeEvent(input$betaCluster_output_code,
...
@@ -142,6 +144,34 @@ observeEvent(input$betaCluster_output_code,
}
}
)
)
## MANOVA
output
$
betaManovaUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
box
(
title
=
"Setting : "
,
width
=
NULL
,
status
=
"primary"
,
selectInput
(
"betaManovaVar"
,
label
=
"Covariates"
,
multiple
=
TRUE
,
choices
=
c
(
sample_variables
(
physeq
())),
selected
=
NULL
)
#,
# actionButton("betaManovaButton",
# "Compute"),
)
})
output
$
betaManova
<-
renderPrint
({
validate
(
need
(
physeq
(),
"Requires an abundance dataset"
))
validate
(
need
(
input
$
betaManovaVar
,
"Requires at least one covariate"
))
vegan
::
adonis
(
as.formula
(
paste
(
"betaDist()"
,
"~"
,
paste
(
input
$
betaManovaVar
,
collapse
=
"*"
))),
data
=
as
(
sample_data
(
physeq
()),
"data.frame"
),
perm
=
9999
)
})
## Heatmap
output
$
betaHeatmapUI
<-
renderUI
({
output
$
betaHeatmapUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
validate
(
need
(
physeq
(),
""
))
box
(
box
(
...
@@ -211,6 +241,7 @@ observeEvent(input$betaHeatmap_output_code,
...
@@ -211,6 +241,7 @@ observeEvent(input$betaHeatmap_output_code,
}
}
)
)
## Network
output
$
betaNetworkUI
<-
renderUI
({
output
$
betaNetworkUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
validate
(
need
(
physeq
(),
""
))
box
(
box
(
...
@@ -275,6 +306,7 @@ observeEvent(input$betaNetwork_output_code,
...
@@ -275,6 +306,7 @@ observeEvent(input$betaNetwork_output_code,
}
}
)
)
## Table
output
$
betaTable
<-
renderUI
({
output
$
betaTable
<-
renderUI
({
validate
(
need
(
physeq
(),
"Requires an abundance dataset"
))
validate
(
need
(
physeq
(),
"Requires an abundance dataset"
))
box
(
box
(
...
...
panels/richnessB-ui.R
View file @
58726f00
...
@@ -2,8 +2,11 @@ betaMds <- fluidPage(outputCodeButton(withLoader(plotOutput("betaMds", height =
...
@@ -2,8 +2,11 @@ betaMds <- fluidPage(outputCodeButton(withLoader(plotOutput("betaMds", height =
uiOutput
(
"betaMdsUI"
))
uiOutput
(
"betaMdsUI"
))
betaCluster
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaCluster"
,
height
=
700
))),
betaCluster
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaCluster"
,
height
=
700
))),
uiOutput
(
"betaClusterUI"
))
uiOutput
(
"betaClusterUI"
))
betaHeatmap
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaHeatmap"
,
height
=
700
))),
betaManova
<-
fluidPage
(
withLoader
(
verbatimTextOutput
(
"betaManova"
)),
uiOutput
(
"betaHeatmapUI"
))
uiOutput
(
"betaManovaUI"
),
verbatimTextOutput
(
"betaManova2"
))
betaNetwork
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaNetwork"
,
height
=
700
))),
betaNetwork
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaNetwork"
,
height
=
700
))),
uiOutput
(
"betaNetworkUI"
))
uiOutput
(
"betaNetworkUI"
))
betaHeatmap
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaHeatmap"
,
height
=
700
))),
uiOutput
(
"betaHeatmapUI"
))
betaTable
<-
fluidPage
(
uiOutput
(
"betaTable"
))
betaTable
<-
fluidPage
(
uiOutput
(
"betaTable"
))
ui.R
View file @
58726f00
...
@@ -69,6 +69,7 @@ dashboardHeader(title = "Easy16S"),
...
@@ -69,6 +69,7 @@ dashboardHeader(title = "Easy16S"),
choices
=
list
(
"bray"
,
"jaccard"
,
"unifrac"
,
"wunifrac"
,
"dpcoa"
,
"jsd"
,
"euclidean"
)),
choices
=
list
(
"bray"
,
"jaccard"
,
"unifrac"
,
"wunifrac"
,
"dpcoa"
,
"jsd"
,
"euclidean"
)),
menuSubItem
(
"MultiDimensional Scaling"
,
tabName
=
"betaMds"
),
menuSubItem
(
"MultiDimensional Scaling"
,
tabName
=
"betaMds"
),
menuSubItem
(
"Samples clustering"
,
tabName
=
"betaCluster"
),
menuSubItem
(
"Samples clustering"
,
tabName
=
"betaCluster"
),
menuSubItem
(
"Multivariate ANOVA"
,
tabName
=
"betaManova"
),
menuSubItem
(
"Network"
,
tabName
=
"betaNetwork"
),
menuSubItem
(
"Network"
,
tabName
=
"betaNetwork"
),
menuSubItem
(
"Samples heatmap"
,
tabName
=
"betaHeatmap"
),
menuSubItem
(
"Samples heatmap"
,
tabName
=
"betaHeatmap"
),
menuSubItem
(
"Table"
,
tabName
=
"betaTable"
)
menuSubItem
(
"Table"
,
tabName
=
"betaTable"
)
...
@@ -91,6 +92,7 @@ dashboardHeader(title = "Easy16S"),
...
@@ -91,6 +92,7 @@ dashboardHeader(title = "Easy16S"),
tabItem
(
tabName
=
"alphaTable"
,
alphaTable
),
tabItem
(
tabName
=
"alphaTable"
,
alphaTable
),
tabItem
(
tabName
=
"betaMds"
,
betaMds
),
tabItem
(
tabName
=
"betaMds"
,
betaMds
),
tabItem
(
tabName
=
"betaCluster"
,
betaCluster
),
tabItem
(
tabName
=
"betaCluster"
,
betaCluster
),
tabItem
(
tabName
=
"betaManova"
,
betaManova
),
tabItem
(
tabName
=
"betaNetwork"
,
betaNetwork
),
tabItem
(
tabName
=
"betaNetwork"
,
betaNetwork
),
tabItem
(
tabName
=
"betaHeatmap"
,
betaHeatmap
),
tabItem
(
tabName
=
"betaHeatmap"
,
betaHeatmap
),
tabItem
(
tabName
=
"betaTable"
,
betaTable
),
tabItem
(
tabName
=
"betaTable"
,
betaTable
),
...
...
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