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Amine GHOZLANE
shaman
Commits
3fedc910
Commit
3fedc910
authored
Sep 20, 2016
by
svolant
Browse files
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parent
a67b11b4
Changes
2
Hide whitespace changes
Inline
Side-by-side
server.R
View file @
3fedc910
...
...
@@ -3,6 +3,7 @@ library(shiny)
renderDataTable
<-
DT
::
renderDataTable
dataTableOutput
<-
DT
::
dataTableOutput
shinyServer
(
function
(
input
,
output
,
session
)
{
hide
(
id
=
"loading-content"
,
anim
=
TRUE
,
animType
=
"fade"
,
time
=
1.5
)
...
...
@@ -185,7 +186,7 @@ shinyServer(function(input, output,session) {
if
(
!
is.null
(
data
$
counts
)
&&
!
is.null
(
data
$
taxo
)
&&
nrow
(
data
$
counts
)
>
0
&&
nrow
(
data
$
taxo
)
>
0
&&
!
is.null
(
taxo
)
&&
taxo
!=
"..."
&&
!
is.null
(
target
))
{
design
=
GetDesign
(
input
)
tmp
=
isolate
(
GetCountsMerge
(
input
,
data
,
taxo
,
target
,
design
))
tmp
=
isolate
(
withProgress
(
GetCountsMerge
(
input
,
data
,
taxo
,
target
,
design
)
,
message
=
"Merging the counts ..."
)
)
counts
=
tmp
$
counts
CheckTarget
=
tmp
$
CheckTarget
#target = tmp$target
...
...
@@ -294,13 +295,9 @@ shinyServer(function(input, output,session) {
menuSubItem
(
"Comparison plots"
,
tabName
=
"CompPlot"
),
tabName
=
"Visu"
),
menuItem
(
"Perspective plots"
,
icon
=
icon
(
"pie-chart"
),
tabName
=
"Krona"
)
)
}
else
{
sidebarMenu
()
}
})
...
...
@@ -333,7 +330,7 @@ shinyServer(function(input, output,session) {
output
$
DataTaxo
<-
renderDataTable
(
dataInput
()
$
data
$
taxo
,
options
=
list
(
lengthMenu
=
list
(
c
(
10
,
50
,
-1
),
c
(
'10'
,
'50'
,
'All'
)),
pageLength
=
10
,
scrollX
=
TRUE
pageLength
=
10
,
scrollX
=
TRUE
,
processing
=
FALSE
))
...
...
@@ -993,29 +990,28 @@ shinyServer(function(input, output,session) {
## Get the results from DESeq2
ResDiffAnal
<-
eventReactive
(
input
$
RunDESeq
,{
ResDiffAnal
<-
eventReactive
(
input
$
RunDESeq
,
withProgress
(
{
target
=
dataInputTarget
()
$
target
design
=
GetDesign
(
input
)
counts
=
d
ataMergeCounts
()
$
counts
CT_noNorm
=
d
ataMergeCounts
()
$
CT_noNorm
CT_Norm
=
d
ataMergeCounts
()
$
CT_Norm
dMC
=
dataMergeCounts
()
counts
=
d
MC
$
counts
CT_noNorm
=
d
MC
$
CT_noNorm
CT_Norm
=
d
MC
$
CT_Norm
## If no file, size factors are estimated
normFactors
=
SizeFactors_fromFile
()
$
normFactors
Get_dds_object
(
input
,
counts
,
target
,
design
,
normFactors
,
CT_noNorm
,
CT_Norm
)
})
}
,
message
=
"Analysis in progress"
)
)
## Run DESeq2 via RunDESeq button
observeEvent
(
input
$
RunDESeq
,{
withProgress
(
message
=
"Analysis in progress..."
,
ResDiffAnal
())
ResDiffAnal
()
})
#####################################################
##
...
...
ui.R
View file @
3fedc910
...
...
@@ -5,7 +5,7 @@ library(shinythemes)
library
(
shinyjs
)
function
(
request
)
{
sidebar
<-
dashboardSidebar
(
useShinyjs
(),
inlineCSS
(
appCSS
),
...
...
@@ -20,6 +20,7 @@ sidebar <- dashboardSidebar(
menuItem
(
"Home"
,
tabName
=
"Home"
,
icon
=
icon
(
"home"
)),
menuItem
(
"Tutorial"
,
tabName
=
"Tutorial"
,
icon
=
icon
(
"book"
)),
menuItem
(
"Upload your data"
,
tabName
=
"Upload"
,
icon
=
icon
(
"upload"
)),
# bookmarkButton(),
menuItemOutput
(
"dymMenu"
),
img
(
src
=
"logo.jpg"
,
height
=
49
,
width
=
220
,
style
=
"position:absolute;bottom:0;margin:0 0 15px 10px;"
)
)
...
...
@@ -714,11 +715,13 @@ body <- dashboardBody(
dbHeader
$
children
[[
2
]]
$
children
<-
tags
$
a
(
tags
$
img
(
src
=
'akuaku.png'
,
height
=
'40'
,
width
=
'50'
,
style
=
"margin:5px 0 5px 0;"
,
align
=
'left'
),
tags
$
h3
(
"SHAMAN"
,
style
=
"font-family:Purisa; margin:15px 25px 5px 0;color:white;"
))
# Put them together into a dashboardPage
dashboardPage
(
skin
=
"blue"
,
dashboardPage
(
skin
=
"blue"
,
dbHeader
,
sidebar
,
body
)
}
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