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Midoux Cedric
easy16S
Commits
ca7904d8
Commit
ca7904d8
authored
Dec 21, 2020
by
Midoux Cedric
Browse files
betaMDS
parent
b02107b9
Changes
6
Hide whitespace changes
Inline
Side-by-side
panels/mds-server.R
deleted
100644 → 0
View file @
b02107b9
output
$
mdsUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
box
(
title
=
"Setting : "
,
width
=
NULL
,
status
=
"primary"
,
checkboxGroupInput
(
"mdsAxes"
,
label
=
"Axes : "
,
choices
=
seq
(
10
),
selected
=
c
(
1
,
2
),
inline
=
TRUE
),
selectInput
(
"mdsDist"
,
label
=
"Distance : "
,
selected
=
"bray"
,
choices
=
list
(
"bray"
,
"jaccard"
,
"unifrac"
,
"wunifrac"
,
"dpcoa"
,
"jsd"
,
"euclidean"
)
),
selectInput
(
"mdsMethod"
,
label
=
"Method : "
,
selected
=
"MDS"
,
choices
=
list
(
"DCA (Detrended Correspondence Analysis)"
=
"DCA"
,
"CCA (Constrained Correspondence Analysis)"
=
"CCA"
,
"RDA (Redundancy Analysis)"
=
"RDA"
,
"CAP (Constrained Analysis of Principal Coordinates)"
=
"CAP"
,
"DPCoA (Double Principle Coordinate Analysis)"
=
"DPCoA"
,
"NMDS (Non-metric MultiDimenstional Scaling)"
=
"NMDS"
,
"MDS / PCoA (Principal Coordinate Analysis)"
=
"MDS"
)
),
textInput
(
"mdsTitle"
,
label
=
"Title : "
,
value
=
"Samples ordination graphic"
),
selectInput
(
"mdsLabel"
,
label
=
"Label : "
,
choices
=
c
(
"..."
=
0
,
sample_variables
(
physeq
()))
),
selectInput
(
"mdsCol"
,
label
=
"Color : "
,
choices
=
c
(
"..."
=
0
,
sample_variables
(
physeq
()))
),
selectInput
(
"mdsShape"
,
label
=
"Shape : "
,
choices
=
c
(
"..."
=
0
,
sample_variables
(
physeq
()))
),
selectInput
(
"mdsEllipse"
,
label
=
"Ellipses : "
,
choices
=
c
(
"..."
=
0
,
sample_variables
(
physeq
()))
)
)
})
output
$
mds
<-
metaRender2
(
renderPlot
,
{
validate
(
need
(
physeq
(),
"Requires an abundance dataset"
),
need
(
length
(
input
$
mdsAxes
)
==
2
,
"Requires two projections axes"
))
data
<-
physeq
()
mdsEllipse
<-
if
(
!
is.null
(
checkNull
(
input
$
mdsEllipse
)))
{
metaExpr
({
stat_ellipse
(
aes_string
(
group
=
..
(
input
$
mdsEllipse
)))
})
}
metaExpr
({
ord
<-
ordinate
(
data
,
method
=
..
(
input
$
mdsMethod
),
distance
=
..
(
input
$
mdsDist
))
p
<-
plot_ordination
(
physeq
=
data
,
ordination
=
ord
,
type
=
"samples"
,
axes
=
..
(
as.numeric
(
input
$
mdsAxes
)),
color
=
..
(
checkNull
(
input
$
mdsCol
)),
shape
=
..
(
checkNull
(
input
$
mdsShape
)),
label
=
..
(
checkNull
(
input
$
mdsLabel
)),
title
=
..
(
checkNull
(
input
$
mdsTitle
))
)
p
<-
p
+
..
(
mdsEllipse
)
p
+
theme_bw
()
})
})
observeEvent
(
input
$
mds_output_code
,
{
displayCodeModal
(
expandChain
(
quote
(
library
(
phyloseq
)),
quote
(
library
(
phyloseq.extended
)),
"# Replace `data` with you own data."
,
output
$
mds
()
)
)
}
)
panels/mds-ui.R
deleted
100644 → 0
View file @
b02107b9
mds
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"mds"
,
height
=
700
))),
uiOutput
(
"mdsUI"
))
panels/richnessB-server.R
View file @
ca7904d8
output
$
betaMdsUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
box
(
title
=
"Setting : "
,
width
=
NULL
,
status
=
"primary"
,
checkboxGroupInput
(
"betaMdsAxes"
,
label
=
"Axes : "
,
choices
=
seq
(
10
),
selected
=
c
(
1
,
2
),
inline
=
TRUE
),
selectInput
(
"betaMdsMethod"
,
label
=
"Method : "
,
selected
=
"MDS"
,
choices
=
list
(
"DCA (Detrended Correspondence Analysis)"
=
"DCA"
,
"CCA (Constrained Correspondence Analysis)"
=
"CCA"
,
"RDA (Redundancy Analysis)"
=
"RDA"
,
"CAP (Constrained Analysis of Principal Coordinates)"
=
"CAP"
,
"DPCoA (Double Principle Coordinate Analysis)"
=
"DPCoA"
,
"NMDS (Non-metric MultiDimenstional Scaling)"
=
"NMDS"
,
"MDS / PCoA (Principal Coordinate Analysis)"
=
"MDS"
)
),
textInput
(
"betaMdsTitle"
,
label
=
"Title : "
,
value
=
"Samples ordination graphic"
),
selectInput
(
"betaMdsLabel"
,
label
=
"Label : "
,
choices
=
c
(
"..."
=
0
,
sample_variables
(
physeq
()))
),
selectInput
(
"betaMdsCol"
,
label
=
"Color : "
,
choices
=
c
(
"..."
=
0
,
sample_variables
(
physeq
()))
),
selectInput
(
"betaMdsShape"
,
label
=
"Shape : "
,
choices
=
c
(
"..."
=
0
,
sample_variables
(
physeq
()))
),
selectInput
(
"betaMdsEllipse"
,
label
=
"Ellipses : "
,
choices
=
c
(
"..."
=
0
,
sample_variables
(
physeq
()))
)
)
})
output
$
betaMds
<-
metaRender2
(
renderPlot
,
{
validate
(
need
(
physeq
(),
"Requires an abundance dataset"
),
need
(
length
(
input
$
betaMdsAxes
)
==
2
,
"Requires two projections axes"
))
data
<-
physeq
()
betaMdsEllipse
<-
if
(
!
is.null
(
checkNull
(
input
$
betaMdsEllipse
)))
{
metaExpr
({
stat_ellipse
(
aes_string
(
group
=
..
(
input
$
betaMdsEllipse
)))
})
}
metaExpr
({
ord
<-
ordinate
(
data
,
method
=
..
(
input
$
betaMdsMethod
),
distance
=
..
(
input
$
betaDistance
))
p
<-
plot_ordination
(
physeq
=
data
,
ordination
=
ord
,
type
=
"samples"
,
axes
=
..
(
as.numeric
(
input
$
betaMdsAxes
)),
color
=
..
(
checkNull
(
input
$
betaMdsCol
)),
shape
=
..
(
checkNull
(
input
$
betaMdsShape
)),
label
=
..
(
checkNull
(
input
$
betaMdsLabel
)),
title
=
..
(
checkNull
(
input
$
betaMdsTitle
))
)
p
<-
p
+
..
(
betaMdsEllipse
)
p
+
theme_bw
()
})
})
observeEvent
(
input
$
betaMds_output_code
,
{
displayCodeModal
(
expandChain
(
quote
(
library
(
phyloseq
)),
quote
(
library
(
phyloseq.extended
)),
"# Replace `data` with you own data."
,
output
$
betaMds
()
)
)
}
)
output
$
betaClusterUI
<-
renderUI
({
validate
(
need
(
physeq
(),
""
))
box
(
...
...
@@ -13,7 +107,6 @@ output$betaClusterUI <- renderUI({
)
})
output
$
betaCluster
<-
metaRender2
(
renderPlot
,
{
validate
(
need
(
physeq
(),
"Requires an abundance dataset"
))
data
<-
physeq
()
...
...
panels/richnessB-ui.R
View file @
ca7904d8
betaMds
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaMds"
,
height
=
700
))),
uiOutput
(
"betaMdsUI"
))
betaCluster
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaCluster"
,
height
=
700
))),
uiOutput
(
"betaClusterUI"
))
betaHeatmap
<-
fluidPage
(
outputCodeButton
(
withLoader
(
plotOutput
(
"betaHeatmap"
,
height
=
700
))),
...
...
server.R
View file @
ca7904d8
...
...
@@ -22,7 +22,6 @@ shinyServer
source
(
"panels/rarefactionCurve-server.R"
,
local
=
TRUE
)
source
(
"panels/richnessA-server.R"
,
local
=
TRUE
)
source
(
"panels/richnessB-server.R"
,
local
=
TRUE
)
source
(
"panels/mds-server.R"
,
local
=
TRUE
)
source
(
"panels/pca-server.R"
,
local
=
TRUE
)
source
(
"panels/tree-server.R"
,
local
=
TRUE
)
...
...
ui.R
View file @
ca7904d8
...
...
@@ -9,7 +9,6 @@ source("panels/heatmap-ui.R", local = TRUE)
source
(
"panels/rarefactionCurve-ui.R"
,
local
=
TRUE
)
source
(
"panels/richnessA-ui.R"
,
local
=
TRUE
)
source
(
"panels/richnessB-ui.R"
,
local
=
TRUE
)
source
(
"panels/mds-ui.R"
,
local
=
TRUE
)
source
(
"panels/pca-ui.R"
,
local
=
TRUE
)
source
(
"panels/tree-ui.R"
,
local
=
TRUE
)
source
(
"panels/Help-ui.R"
,
local
=
TRUE
)
...
...
@@ -68,12 +67,12 @@ dashboardHeader(title = "Easy16S"),
selectInput
(
"betaDistance"
,
label
=
"Distance : "
,
choices
=
list
(
"bray"
,
"jaccard"
,
"unifrac"
,
"wunifrac"
,
"dpcoa"
,
"jsd"
,
"euclidean"
)),
menuSubItem
(
"MultiDimensional Scaling"
,
tabName
=
"betaMds"
),
menuSubItem
(
"Samples clustering"
,
tabName
=
"betaCluster"
),
menuSubItem
(
"Samples heatmap"
,
tabName
=
"betaHeatmap"
),
menuSubItem
(
"Network"
,
tabName
=
"betaNetwork"
),
menuSubItem
(
"Table"
,
tabName
=
"betaTable"
)
),
menuItem
(
"MultiDimensional Scaling"
,
tabName
=
"mds"
,
icon
=
icon
(
"dot-circle"
)),
menuItem
(
"PCA"
,
tabName
=
"pca"
,
icon
=
icon
(
"bullseye"
)),
menuItem
(
"Phylogenetic tree"
,
tabName
=
"tree"
,
icon
=
icon
(
"tree"
)),
menuItem
(
"Help"
,
tabName
=
"Help"
,
icon
=
icon
(
"info-circle"
))
...
...
@@ -90,11 +89,11 @@ dashboardHeader(title = "Easy16S"),
tabItem
(
tabName
=
"rarefactionCurve"
,
rarefactionCurve
),
tabItem
(
tabName
=
"alphaPlot"
,
alphaPlot
),
tabItem
(
tabName
=
"alphaTable"
,
alphaTable
),
tabItem
(
tabName
=
"betaMds"
,
betaMds
),
tabItem
(
tabName
=
"betaCluster"
,
betaCluster
),
tabItem
(
tabName
=
"betaHeatmap"
,
betaHeatmap
),
tabItem
(
tabName
=
"betaNetwork"
,
betaNetwork
),
tabItem
(
tabName
=
"betaTable"
,
betaTable
),
tabItem
(
tabName
=
"mds"
,
mds
),
tabItem
(
tabName
=
"pca"
,
pca
),
tabItem
(
tabName
=
"tree"
,
tree
),
tabItem
(
tabName
=
"Help"
,
Help
)
...
...
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